Methods for the assessment of colorectal cancer and colorectal polyps by measurement of metabolites in urine

ABSTRACT

Methods for the diagnosis of CRC, colorectal polyps in general and adenomatous polyps in particular by measurement of metabolites in urine are described. In some embodiments, certain metabolites are identified as being elevated or reduced in concentration or quantity in subjects with CRC and/or colorectal polyps as compared with subjects without CRC or colorectal polyps. The measurement of these metabolites in urine can indicate the presence of CRC or colorectal polyps in general or adanomatous polyps in particular in a subject.

FIELD OF THE INVENTION

This invention relates to the assessment of colorectal cancer andcolorectal polyps by measurement of metabolites in urine.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is the U.S. National Stage of International ApplicationPCT/CA2011/050315 filed May 20, 2011, which designates the U.S. and waspublished by the International Bureau in English on Nov. 24, 2011, andwhich claims the benefit of U.S. Provisional Application No. 61/347,043,filed May 21, 2010, both of which are hereby incorporated by referencein its entirety.

BACKGROUND

Colorectal Cancer (CRC) is among the leading causes of morbidity. Thechance of surviving CRC is closely related to the stage of the diseaseat diagnosis; the earlier the diagnosis, the greater the likelihood ofsurvival. In many instances CRC is preceded by colorectal polyps,particularly adenomatous colorectal polyps. If identified early at thecolorectal polyp or precancerous lesion stage, CRC is more likely to becurable. Therefore, subjects with CRC and/or colorectal polyps wouldgreatly benefit from early diagnosis.

Current CRC screening methods consist of one or a combination of thefollowings: fecal occult blood testing (FOBT), flexible sigmoidoscopy,air-contrast barium enema, computerized tomography colonography (CTC)and/or colonoscopy. These current screening methods all have limitationsor potential risks that limit their application.

Colonoscopy is currently the standard test for the presence or absenceof CRC or colorectal polyps. However, colonoscopy is invasive and canimpose unnecessary hazards and risks caused by sedation or the procedureitself. A known non-invasive CRC diagnostic method is FOBT. FOBT,however, has very low sensitivity in detection of CRC and isunattractive as the handling of fecal matter is required. CTC is arecent non-invasive technique for imaging the colon. However, itsperformance varies due primarily to technological differences in thesubject preparation and the hardware and software used for the analysis.Several new screening methods based on DNA analysis are now available.These are typically PCR-based assays used to identify mutations known tooccur in the adenoma-to-carcinoma sequence, or in familial CRC. However,whether genomics-based tests will result in high diagnostic accuracy forsporadic CRC remains to be seen.

Accordingly, there is a need to develop improved methods of assessingCRC and colorectal polyps in a subject.

SUMMARY

Methods for the diagnosis of CRC, colorectal polyps in general andadenomatous polyps in particular by measurement of metabolites in urineare described. In some embodiments, certain metabolites are identifiedas being elevated or reduced in concentration or quantity in subjectswith CRC and/or colorectal polyps as compared with subjects without CRCor colorectal polyps. The measurement of these metabolites in urine canindicate the presence of CRC or colorectal polyps in general oradanomatous polyps in particular in a subject.

In one aspect, the invention provides a method for assessing whether asubject has or is predisposed to developing CRC and/or colorectalpolyps, said method comprising:

-   (a) providing a urine sample from said subject;-   (b) obtaining a metabolite profile from said urine sample;-   (c) comparing said metabolite profile with a reference metabolite    profile; and-   (d) assessing, based on said comparison in step (c), whether said    subject has or is predisposed to developing CRC and/or colorectal    polyps.

A further aspect of the invention relates to a method for identifyingurine metabolites indicative of the presence or absence of CRC and/orcolorectal polyps, said method comprising:

(a) providing a urine sample from a subject;

(b) obtaining a metabolite profile from said urine sample;

(c) comparing said metabolite profile with a reference metaboliteprofile; and

(d) identifying, based on said comparison in step (c), one or moremetabolites in said metabolite profile that are indicative of thepresence of or predisposition to in said subject of CRC and/orcolorectal polyps.

A further aspect of the invention relates to a use of a urine metaboliteprofile comprising one or more of metabolites selected from the groupconsisting of:

-   -   1,6-Anhydro-β-D-glucose, 1-Methylnicotinamide,        2-Hydroxyisobutyrate, 2-Oxoglutarate, 3-Aminoisobutyrate,        3-Hydroxybutyrate, 3-Hydroxyisovalerate, 3-Hydroxymandelate,        3-Hydroxyphenylacetate, 3-Indoxylsulfate,        4-Hydroxyphenylacetate, Acetate, Acetone, Adipate, Alanine,        Ascorbate, Asparagine, Benzoate, Betaine, Butyrate, Carnitine,        Citrate, Creatine, Creatinine, Dimethylamine, Ethanol, Formate,        Galactose, Glucose, Glutamine, Glycerol, Glycine, Glycolate,        Guanidoacetate, Hippurate, Histidine, Hypoxanthine, Isoleucine,        Lactate, Leucine, Lysine, Mannitol, Methanol, Methylguanidine,        N,N-Dimethylglycine, O-Acetylcarnitine, Pantothenate, Propylene        glycol, Pyroglutamate, Pyruvate, Serine, Succinate, Sucrose,        Tartrate, Taurine, Threonine, Trigonelline, Trimethylamine,        Trimethylamine N-oxide, Tyrosine, Uracil, Urea, Valine, Xylose,        cis-Aconitate, β-Alanine, H-Methylhistidine, T-Methylhistidine        and trans-Aconitate,        for assessing whether a subject has or is predisposed to        developing CRC and/or colorectal polyps.

A further aspect of the invention relates to a kit for assessing whethera subject has or is predisposed to developing CRC and/or colorectalpolyps, said kit comprising one or more reagents for detecting thepresence and/or concentration and/or amount of one or more metabolitesin a urine sample of a subject, and instructions for use of said kit forassessing whether a subject has or is predisposed to developing CRCand/or colorectal polyps.

A further aspect of the invention relates to a system comprising:

(a) a CRC- and/or colorectal polyps-assessing apparatus including acontrol unit and a memory unit to assess a CRC state in a subject; and

(b) an information communication terminal apparatus that provides dataon the presence and/or concentration and/or amount of metabolites in aurine sample from the subject connected to each other communicatively,

wherein the information communication terminal apparatus includes:

(a) a data sending unit that transmits the data on the presence and/orconcentration and/or amount of metabolites in the sample to the CRC-and/or colorectal polyps-assessing apparatus; and

b) an assessment result-receiving unit that receives the assessmentresult of the CRC and/or colorectal polyps state of the subjecttransmitted from the CRC- and/or colorectal polyps-assessing apparatus,

wherein the control unit of the CRC- and/or colorectal polyps-assessingapparatus includes:

(a) a data-receiving unit that receives the data on the metaboliteconcentration and/or amount of the sample transmitted from theinformation communication terminal apparatus;

(b) a discriminant value-calculating unit that calculates a discriminantvalue that is a value of multivariate discriminant, based on both theconcentration and/or amount value of the metabolite in the samplereceived by the data-receiving unit and a multivariate discriminant withthe concentration and/or amount of the metabolite as explanatoryvariable stored in the memory unit;(c) a discriminant value criterion-assessing unit that assesses the CRCor colorectal polyps state in the subject, based on the discriminantvalue calculated by the discriminant value-calculating unit; and(d) an assessment result-sending unit that transmits the assessmentresult of the subject obtained by the discriminant valuecriterion-assessing unit to the information communication terminalapparatus.

A further aspect of the invention relates to a method for identifyingand evaluating effectiveness of pharmaceutical agents and/or surgicaltreatments and/or physical treatments against CRC and/or colorectalpolyps, said method comprising:

(a) providing a first urine sample from a subject having CRC orcolorectal polyps;

(b) obtaining a metabolite profile from said first urine sample;

(c) administering one or more pharmaceutical candidates and/orperforming one or more physical or surgical treatments to or on saidsubject;

(d) providing a second urine sample from said subject in step (c);

(e) obtaining a metabolite profile from said second urine sample;

(f) comparing said metabolite profile obtained in steps (b) and (e) witha reference metabolite profile; and

(g) assessing, based on said comparison in step (f), whether the one ormore pharmaceutical candidates and/or treatments is effective againstCRC and/or colorectal polyps.

BRIEF DESCRIPTION OF THE DRAWINGS

In the drawings, which illustrate embodiments of the invention by way ofexample only:

FIG. 1 is a variable importance in the projection (VIP) plot of analyzedmetabolites in order of their contribution to the separation betweendata from urine samples obtained from subjects having CRC and that fromsubjects without CRC and/or colorectal polyps for 69 metabolites;

FIG. 2 is a VIP plot of analyzed metabolites in order of theircontribution to the separation between data from urine samples obtainedfrom subjects having CRC and that from subjects without CRC and/orcolorectal polyps for 20 metabolites with a VIP value higher than 1;

FIG. 3 is a 2-dimensional orthogonal partial least square (OPLS) scatterplot of the data from urine samples obtained from subjects without CRCand/or colorectal polyps (grey squares) compared to that from subjectshaving CRC (black dots) constructed from 69 metabolites;

FIG. 4 is a 2-dimensional OPLS scatter plot of the data from urinesamples obtained from subjects without CRC and/or colorectal polyps(grey squares) compared to that from subjects having CRC (black dots)constructed from 20 metabolites with a VIP value higher than 1;

FIG. 5 is a 2-dimensional partial least square discriminant analysis(PLS-DA) scatter plot of the data from urine samples obtained fromsubjects without CRC and/or colorectal polyps (grey squares) compared tothat from subjects having CRC (black dots) constructed from 69metabolites;

FIG. 6 is a 2-dimensional PLS-DA scatter plot of the data from urinesamples obtained from subjects without CRC and/or colorectal polyps(grey squares) compared to that from subjects having CRC (black dots)constructed from 20 metabolites with a VIP value higher than 1;

FIG. 7 is an observed versus predicted plot of the OPLS model of FIG. 3.Data from urine sample obtained from subjects without CRC and/orcolorectal polyps is displayed as grey squares and that from subjectshaving CRC is displayed as black dots;

FIG. 8 is an observed versus predicted plot of the OPLS model of FIG. 4.Data from urine sample obtained from subjects without CRC and/orcolorectal polyps is displayed as grey squares and that from subjectshaving CRC is displayed as black dots;

FIG. 9 is a receiver operating characteristics (ROC) curve of the OPLSmodel of FIG. 3;

FIG. 10 is a ROC curve of the OPLS model of FIG. 4;

FIG. 11 is a VIP plot of analyzed metabolites in order of theircontribution to the separation between the data from urine samplesobtained from subjects without CRC and/or colorectal polyps and thatfrom subjects having colorectal polyps for 69 metabolites;

FIG. 12 is a VIP plot of analyzed metabolites in order of theircontribution to the separation between the data from urine samplesobtained from subjects without CRC and/or colorectal polyps and thatfrom subjects having colorectal polyps for 26 metabolites with a VIPvalue higher than 1;

FIG. 13 is a 2-dimensional OPLS plot of the data from urine samplesobtained from subject without CRC and/or colorectal polyps (greysquares) compared to that from subjects having colorectal polyps (blackdiamonds) constructed from 69 metabolites;

FIG. 14 is a 2-dimensional OPLS plot of the data from urine samplesobtained from subject without CRC and/or colorectal polyps (greysquares) compared to that from subjects having colorectal polyps (blackdiamonds) constructed from 26 metabolites with a VIP value higher than1;

FIG. 15 is a 2-dimensional PLS-DA scatter plot of the data from urinesamples obtained from subjects without CRC and/or colorectal polyps(grey squares) compared to that from subject having colorectal polyps(black diamonds) constructed from 69 metabolites;

FIG. 16 is a 2-dimensional PLS-DA scatter plot the data from urinesamples obtained from subjects without CRC and/or colorectal polyps(grey squares) compared to that from subject having colorectal polyps(black diamonds) constructed from 26 metabolites with a VIP value higherthan 1;

FIG. 17 is an observed versus predicted plot of the OPLS model of FIG.13. Data from urine samples obtained from subjects without CRC and/orcolorectal polyps are displayed as grey squares and that from subjectshaving colorectal polyps are displayed as black diamonds;

FIG. 18 is an observed versus predicted plot of the OPLS model of FIG.14. Data from urine samples obtained from subjects without CRC and/orcolorectal polyps are displayed as grey squares and that from subjectshaving colorectal polyps are displayed as black diamonds;

FIG. 19 is a ROC curve of the OPLS model of FIG. 13;

FIG. 20 is a ROC curve of the OPLS model of FIG. 14;

FIG. 21 is a VIP plot of analyzed metabolites in order of theircontribution to the separation between the data from urine samplesobtained from subjects without CRC and/or colorectal polyps and thatfrom the group of subjects having adenomatous polyps for 69 metabolites;

FIG. 22 is a VIP plot of analyzed metabolites in order of theircontribution to the separation between the data from urine samplesobtained from subjects without CRC and/or colorectal polyps and thatfrom subjects having adenomatous polyps for 17 metabolites with a VIPvalue higher than 1;

FIG. 23 is a 2-dimensional OPLS plot of the data from urine samplesobtained from subjects without CRC and/or colorectal polyps (greysquares) compared to that from subjects having adenomatous polyps (blackdiamonds) constructed from 69 metabolites;

FIG. 24 is an observed versus predicted plot of the OPLS model of FIG.23. Data from urine samples obtained from subjects without CRC and/orcolorectal polyps are displayed as grey squares and that from subjectshaving adenomatous polyps are displayed as black diamonds;

FIG. 25 is an observed versus predicted plot of the OPLS model of the2-dimensional OPLS plot with 17 metabolites with a VIP value higherthan 1. The 2-dimensional OPLS plot was prepared based on the data fromurine samples obtained from subjects without CRC and/or colorectalpolyps compared to that from subjects having adenomatous polyps. Datafrom urine samples obtained from subjects without CRC and/or colorectalpolyps are displayed as grey squares and that from subjects havingadenomatous polyps are displayed as black diamonds;

FIG. 26 is a ROC curve of the OPLS model of FIG. 23;

FIG. 27 is a ROC curve of the OPLS model of the 2-dimensional OPLS plotwith 17 metabolites with a VIP value higher than 1. The 2-dimensionalOPLS plot was prepared based on the data from urine samples obtainedfrom subjects without CRC and/or colorectal polyps compared to that fromsubjects having adenomatous polyps;

FIG. 28 is a 2-dimensional OPLS plot based on the data from urinesamples obtained from subjects without CRC and/or colorectal polyps(triangles) compared to that from subjects having adenomatous polyps(diamonds), superimposed with that from subjects having hyperplasticpolyps (squares), constructed from 69 metabolites;

FIG. 29 is a diagram of the invention that provides a system forassessing whether a subject has or is predisposed to developing CRCand/or colorectal polyps; and

FIG. 30 is an overview of the O2PLS model relating two data tables toeach other.

DETAILED DESCRIPTION

CRC and Colorectal Polyps

CRC is among the leading causes of morbidity. CRC is the third mostcommon malignancy in the world, and represents approximately ten percentof the world's total cancer incidence. CRC appears not only in humansbut also in animal species, and in both sexes. Among human beings, morethan 9 out of 10 people diagnosed with CRC are over the age of 50.However, younger individuals can develop CRC.

The chance of surviving CRC is closely related to the stage of thedisease at diagnosis. The likelihood of survival is greater if thediagnosis is made earlier, permitting earlier treatment. Adenomatous andsome other types of colorectal polyps may progress to malignantcarcinomas and may thus be indicative that a subject is at risk ofdeveloping CRC. Thus, not only is it beneficial to be able to detect CRCitself, it is useful to be able to detect also the presence ofprecancerous lesions such as colorectal polyps.

There are a number of types of colorectal polyps. Adenomatous polyps areknown to be a precursor to full-blown CRC. Other types of polyps may notthemselves have malignant potential. Nevertheless, they may be usefulindicators that a subject is at risk of developing CRC. For instance,unlike adenomatous polyps, hyperplastic polyps have been historicallyrecognized as benign growths of the colon that have no malignantpotential—i.e. they were thought to be innocent bystanders. However,hyperplastic polyps have been noted to be more prevalent in populationswith a higher incidence of cancer. Moreover, hyperplastic polyps mayrepresent a heterogenous group of polyps, some of which have significantrisk for malignant potential. These potentially malignant lesions areknown as sessile serrated adenoma and have been linked to themicrosatellite instability cancer pathway and thus are potentialprecursors of sporadic microsatellite unstable CRC.

Currently, the risk factors for CRC are not well understood and fewspecific risk factors other than diet have been established for thedisease. As such, CRC is typically diagnosed from a complete subjecthistory and physical examination, followed by endoscopic and/orradiological imaging. The diagnosis is confirmed with histopathologicalexamination of biopsies or surgically removed specimens.

Current CRC screening methods consist of one or a combination of thefollowings: FOBT, flexible sigmoidoscopy, air-contrast barium enema, CTCand colonoscopy. These current screening methods all have limitations orpotential risks that limit their application.

Colonoscopy is currently the standard test for assessing the presence orabsence of CRC and/or colorectal polyps. However, colonoscopy isinvasive and can impose unnecessary hazards and risks to an individualcaused by sedation or the procedure itself, and complications withcolonoscopy can include perforation, hemorrhage, respiratory depression,arrhythmias, and infection. In addition, it requires considerablephysical resources and skilled personnel.

A known non-invasive CRC diagnostic method is FOBT. FOBT, however, hasvery low sensitivity in detection of CRC. FOBT is based on theassumption that cancers will bleed, therefore, can be detected in thestool using chemical or immunological assays, and involves a crude testfor the peroxidase-like activity of heme in hemoglobin. However, thesensitivity of the test is only approximately 50%, with a 20%sensitivity for adenomas, due to the fact that not all adenomas and CRCsbleed. In addition, it is an unattractive test for subjects as thehandling of fecal matter is required.

CTC, or virtual colonoscopy, is a recent non-invasive technique forimaging the colon. However, its performance varies due primarily totechnological differences in the subject preparation and the hardwareand software used for the analysis. Other limitations of CTC includehigh false positives (FP) readings, inability to detect flat adenomas,no capacity to remove polyps, repetitive and cumulative radiation doses,and cost.

With advances in the CRC related molecular pathology, several newscreening methods based on DNA analysis from stool samples becameavailable. These are typically PCR-based assays used to identifymutations known to occur in the adenoma-to-carcinoma sequence, or infamilial CRC. Commonly screened gene mutations include KRAS, TP53, APC,as well as assays for micro satellite instability and hypermethylatedDNA. However, whether genomics-based tests will result in highdiagnostic accuracy for sporadic CRC remains to be seen.

Metabolomics and Diagnosis of CRC or Colorectal Polyps

Metabolomics is an emerging field of research downstream from genomics,proteomics and transcriptomics. A metabolome is a quantitativecollection of low molecular weight compounds, such as metabolicsubstrates and products, lipids, small peptides, vitamins, and otherprotein cofactors, generated by metabolism. A metabolome is downstreamfrom a transcriptome and a proteome and thus any changes from a normalstate are amplified and are numerically more tractable. Metabolomics canbe a precise, consistent, and quantitative tool to examine and describecellular growth, maintenance, and function.

Metabolomics can be performed on urine, serum, tissue, and even onsaliva and amniotic fluid. Generally, urine metabolomics represents amuch less invasive method of testing compared to tissue or serummetabolomics.

The present invention uses urine metabolomics to identify subjectshaving or at risk of developing CRC and/or colorectal polyps. This isbeneficial in the management of the risk of CRC and/or colorectalpolyps, both in prevention and treatment. The use of urine metabolomicsin the present invention has a number of potential benefits. Obtaining aurine sample and its analysis are relatively simple, non-invasive, andcost efficient compared to the existing methods for assessing presenceor absence of CRC or colorectal polyps. The invention also permitsmonitoring of individual susceptibility to CRC prior to resorting to, orin combination with, conventional screening methods, and provides forpopulation-based monitoring of CRC and/or colorectal polyps.

A wide range of analytical techniques to assay and quantitate componentsof a metabolome and to extract useful metabolite profiles from the dataare available, including e.g. liquid and gas chromatography coupled withmass spectrometry (LCMS or GCMS), nuclear magnetic resonance (NMR)spectroscopy, high performance liquid chromatography (HPLC), thin layerchromatography (TLC), electrochemical analysis, refractive indexspectroscopy, ultra-violet spectroscopy, fluorescent analysis,radiochemical analysis, near-infrared spectroscopy and light scatteringanalysis. The outputs from such analytical techniques can be furtheranalyzed using multivariate analysis such as principal componentanalysis (PCA), partial least squares discriminant analysis (PLS-DA) andorthogonal partial least squares (OPLS).

One or more metabolite profiles obtained from the previously describedanalysis based on a reference population of known CRC and/or colorectalpolyp status can be used as a reference to assess the presence orabsence of CRC or colorectal polyps in a subject. For example, areference population may be composed of healthy subjects (i.e. subjectsknown or assessed by other means to be free of CRC and/or colorectalpolyps), or alternatively may be composed of subjects already identifiedto have or to be predisposed to developing CRC or colorectal polyps.This assessment can be performed by: (a) providing a urine sample from asubject that is suspected to have or be predisposed to developing CRCand/or colorectal polyps; (b) obtaining a metabolite profile from saidurine sample; (c) comparing said metabolite profile with a referencemetabolite profile; and (d) assessing, based on said comparison in step(c), whether said subject has or is predisposed to developing CRC and/orcolorectal polyps.

Providing and Processing Urine Samples

Urine samples can be collected from subjects that are known or suspectedto have CRC or colorectal polyps, and from subjects without CRC orcolorectal polyps, by known protocols. The subjects of this inventioninclude both sexes of animal species that are susceptible to CRC and/orcolorectal polyps, including humans.

In addition to providing a urine sample, subjects can take a FOBT, fecalimmune testing (FIT), and/or a colonoscopy, the results of which can beused to determine classification of subjects into one of the groups of:subjects without CRC and/or colorectal polyps (normal group); subjectshaving colorectal polyps in general (polyp group); or subjects havingadenomatous polyps specifically (adenomatous group). Pathology ofresected surgical specimens can be used as the standard to classifysubjects into a group where subjects have CRC (CRC group). Relevantclinical information such as age, gender, family history, comorbidities,medications etc. can be obtained from study questionnaires and subjects'medical charts, which could also be used to determine classification ofsubjects. Such testing can be used in the development of reference urinemetabolite profiles and can also be used as an adjunct to screening testsubjects by the methods of the invention to confirm or further refine adiagnosis of CRC and/or colorectal polyps.

Urine samples can be collected from subjects any time, e.g. duringroutine screening or in connection with a regular check-up or visit to aphysician, or prior to or together with administration of treatment,such as the administration of a medicine or performance of surgery.Urine samples can be collected one or more times for a separate orcombined analysis, e.g. 15-700 ml each time. Urine sample collectioncontainers can vary in size and shape, but ideally can accommodate e.g.20-1,000 ml of urine sample. Typically, the container is sterile. Ifdesired, sample containers can be pre-filled or treated with agents forpreventing contamination of the sample by microorganisms such asbacteria and fungi while a sample is waiting to be stored, or suchagents can be added after sample collection. Metabolomic analysis of thecollected urine samples may occur immediately or the samples may beprocessed for storage and later analysis. For example, the whole or partof the sample could be stored in a freezer at −5˜10° C. within 0˜48hours of collection, or could be frozen at −120˜−10° C. within 0-48hours of collection, or could be processed with chemicals for futureanalysis or use before being stored. If samples have been stored frozen,they may be thawed (e.g. at room temperature for 12-48 hours), prior toanalysis.

Obtaining a Metabolite Profile from the Sample

The analytical techniques that make it possible to obtain metaboliteprofiles from the urine samples can include one or a combination of, butnot limited to, mass spectrometry (MS) coupled with gas chromatography(GCMS) or liquid chromatography (LCMS), HPLC, NMR spectroscopy, TLC,electrochemical analysis, refractive index spectroscopy, ultra-violetspectroscopy, fluorescent analysis, radiochemical analysis,near-infrared spectroscopy and light scattering analysis. The outputsobtained from such analyses can be further analyzed using multivariatestatistical analysis to aid in the characterization of differences ofmetabolite profile between samples related to CRC or colorectal polyps.Such analytical tools include, but are not limited to, principalcomponent analysis (PCA), partial least squares discriminant analysis(PLS-DA) and orthogonal partial least squares (OPLS). Though HPLC ortechnologies involving MS can be used for measuring metaboliteconcentrations in the sub-molar range, they are often laborious and timeconsuming as they require that chromatography (liquid or gas) toseparate the metabolites be done first, and also require multipleinternal standards.

NMR spectroscopy is an ideal tool for metabolonomics study because itcan quantify a large number of metabolites simultaneously, requires onlyone standard, and is generally faster to yield statistical analysisresults such as PCA and/or OPLS plots.

In some embodiments, urine samples may be processed prior to analysis.For example, for non-automated (manual) NMR acquisition, about 100-1,000μL urine sample can be taken from the collected and/or stored sample,then diluted with an internal standard at a ratio of e.g. 1:1-1:20(v/v). The internal standard can include e.g. 1-20 mM of sodium2,2-dimethyl-2-silapentane-5-sulfonate (DSS) or its salt form,4,4-Dimethyl-4-silapentane-1-ammonium trifluoroacetate (DSA), orTrimethylsilyl propionate (TSP). Agents for preventing microbialcontamination can also be added. Such additions can include e.g. 10-200mM imidazole, or 0.1-0.5% or 0.5-5 μM of sodium azide. The total volumecan be e.g. 100-1,300 μL. The sample for NMR analysis can be stored in afreezer at e.g. 1-6° C. The same process applies to the automated(robotic) NMR acquisition. On the day of NMR acquisition, the pH of eachsample is measured. Various concentrations of acids and bases, forexample, but not limited to, HCl and NaOH, can be added to the samplesto achieve a pH between e.g. 6.7 and 6.8 to minimize chemical exchangeas the chemical shift can change with pH. An aliquot of e.g. 100-1,000μL of the samples can be placed in NMR tubes and capped for the samplesfor both non-automated and the automated NMR.

One-dimensional NMR spectra can be acquired. After the spectra areobtained, the pH of each sample can be rechecked to ensure that the pHhas not shifted a significant amount. This data can be recorded to bereferenced if a particular sample would produce an unexpected spectrum.Samples can be frozen and stored again at a sub-zero temperature.

Identification of Metabolites for a Reference Metabolite Profile

The present invention involves the discovery that metabolite profiles inthe urine of subjects having or predisposed to developing CRC and/orcolorectal polyps can be reliably distinguished from metabolite profilesin the urine of healthy subjects (i.e. those without CRC and/orcolorectal polyps) such that this distinction can be used to assesswhether a particular subject has or is predisposed to developing CRCand/or colorectal polyps. One or more reference profiles concerningmetabolites present in the urine of a reference population known eitherto be free of CRC and/or colorectal polyps or to have or be predisposedto developing CRC or colorectal polyps is developed, which can then beused for comparison against a corresponding metabolite profile generatedfrom the urine of a test subject. By analyzing the metabolite content ofurine of subjects of known CRC or colorectal polyp status, it is thenpossible to compare this to the content of the same metabolites insubjects of a different CRC or colorectal polyp status, thus identifyingmetabolites which correlate significantly with the CRC or colorectalpolyp status of an individual. In the illustrative examples herein, 240metabolites were considered and 69 found to be of particularsignificance. However, urine contains thousands of metabolites, and thetechniques described can be employed to assess whether other urinemetabolites are similarly diagnostic of CRC and/or colorectal polyps.

Thus, in one aspect, the invention provides a method for identifyingurine metabolites indicative of the presence or absence of CRC and/orcolorectal polyps, the method comprising: (a) providing a urine samplefrom a subject; (b) obtaining a metabolite profile from the urinesample; (c) comparing the metabolite profile with a reference metaboliteprofile; and (d) identifying, based on the comparison in step (c), oneor more metabolites in the metabolite profile that are indicative of thepresence of or predisposition to in said subject of colorectal cancerand/or colorectal polyps.

Quantification of metabolites, e.g. by concentration or in absoluteamount, can be done once the analysis data is available from, forexample, but not limited to, GCMS, LCMS, HPLC, NMR spectroscopy, TLC,electrochemical analysis, refractive index spectroscopy, ultra-violetspectroscopy, fluorescent analysis, radiochemical analysis,near-infrared spectroscopy and light scattering analysis. Thequantification data can be used to identify and to set a standard todetermine a reference metabolite profile based on urine samples obtainedfrom subjects known to be free of CRC and/or colorectal polyps.

For example, once the spectra are acquired from NMR spectroscopy,quantification of metabolites can be done using tools that compare theintegral of a known reference signal, such as DSS, DSA or TSP, withsignals derived from a library of compounds to determine concentrationrelative to the reference signal. The tools can include softwares suchas Chenomx NMRSuite v4.6 software. The quantification process can bedone by more than one individual for reading and verification tooptimize accuracy.

Levels of the specific metabolites over or below a determined criticalvalue, either in concentration or in amount, can indicate the presenceof CRC or colorectal polyps in general or adenomatous polyps inparticular. The concentrations or the amount of the metabolites can beinterpreted independently using an individual cut-off for eachmetabolite or they can be interpreted collectively. Metaboliteconcentrations or amounts obtained can be used as they are (i.e. as theraw data) or be normalized. For example, the concentration or amount ofa metabolite can be log-transformed to normalize the concentrations oramounts to the concentration or the amount of other metabolites. Themetabolites can also be normalized to the concentration of allmetabolites minus the concentration of selected compounds such as e.g.urea to obtain similar results.

Those metabolites which are not products of normal metabolism of asubject (e.g. xenobiotics such as ibuprofen and salicylurate) orinternal standards (e.g. DSS) can be excluded in the analysis.

Multivariate statistical analysis can be applied to the collected dataor complex spectral data to identify differences arising between thegroups of data sets obtained from the urine sample. The metabolitemeasurements in samples from subject having CRC or colorectal polyps ingeneral or adenomatous polyps specifically can be compared to metabolitemeasurements in samples from subjects without CRC or colorectal polypsto identify metabolites that significantly contribute to the separationof different groups. Data comparison can be performed using anyappropriate tools that fulfill the purpose. The tools include PCA,PLS-DA, OPLS and support vector machines (SVM), and softwares that canperform one or more of such analyses, e.g., Simca-P+, can be used. Theseare statistical methods of compressing multidimensional data down to twoor three main components. PLS-DA and OPLS are supervised, that is, theytake into account the class assignments, while PCA is unsupervised andcan be influenced by many factors such as gender, comorbidities etc.

An optimized multivariate cut-off for the underlying combination ofmetabolites can be used to discriminate a cancerous or pre-cancerousstate from a healthy state. Upon determination of which specificmetabolites are the significant contributors to the data separationbetween the CRC group and the normal group samples or the polyp groupand the normal group samples or the adenoma group and the normal groupsamples, one or more profiles of these specific metabolites can beestablished. One or more metabolite profiles or its combination can beused as a reference metabolite profile to assess CRC or colorectalpolyps in general or adenomatous polyps in particular in a subject.

In some embodiments, metabolites that were significant in separatingnormal group from CRC group, normal group from polyp group, and normalgroup from adenoma group were identified as: 1,6-Anhydro-β-D-glucose;1-Methylnicotinamide; 2-Hydroxyisobutyrate; 2-Oxoglutarate;3-Aminoisobutyrate; 3-Hydroxybutyrate; 3-Hydroxyisovalerate;3-Hydroxymandelate; 3-Hydroxyphenylacetate; 3-Indoxylsulfate;4-Hydroxyphenylacetate; Acetate; Acetone; Adipate; Alanine; Ascorbate;Asparagine; Benzoate; Betaine; Butyrate; Carnitine; Citrate; Creatine;Creatinine; Dimethylamine; Ethanol; Formate; Galactose; Glucose;Glutamine; Glycerol; Glycine; Glycolate; Guanidoacetate; Hippurate;Histidine; Hypoxanthine; Isoleucine; Lactate; Leucine; Lysine; Mannitol;Methanol; Methylguanidine; N,N-Dimethylglycine; O-Acetylcarnitine;Pantothenate; Propylene glycol; Pyroglutamate; Pyruvate; Serine;Succinate; Sucrose; Tartrate; Taurine; Threonine; Trigonelline;Trimethylamine; Trimethylamine N-oxide; Tyrosine; Uracil; Urea; Valine;Xylose; cis-Aconitate; β-Alanine; H-Methylhistidine; T-Methylhistidine;and trans-Aconitate.

However, not all features of the metabolite analysis results are alwaysrequired for a proper diagnosis of CRC, colorectal polyps in general oradenomatous polyps specifically. Since there would be an incrementalcost to obtaining more information about a subject's urine metaboliteprofile, it may be beneficial to use the minimal number of metabolitespossible. In order to determine which specific metabolites are thestrongest contributors to the data separation between the CRC group andthe normal group samples or the polyp group and the normal group samplesor the adenoma group and the normal group samples, further data analysiscan be performed. This further data analysis could be made by anappropriate analytical method such as, but not limited to, a VIP plot.

The VIP plot allows identification of metabolites that have a greaterimpact on driving the separation between groups in models. Eachmetabolite used to construct models can be assigned a VIP score. Thisscore is assigned through a statistical formula that is used tocalculate the influence of each metabolite. The higher the VIP score,the greater the influence of the metabolite with the score on separatingdifferent groups. The VIP plot also allows for the comparison of theinfluence of one metabolite to another's. In VIP plot analysis, factorswith a large VIP, usually greater than 1, are said to be the mostrelevant. Metabolites with a VIP value higher than 1 can be thestrongest contributors, and all or part of them can constitute areference metabolite profile once its capability of assessing CRC orcolorectal polyps is successfully demonstrated thorough a comparisonwith the reference metabolite profile consisting of all the metabolitesfound significant in the separation of different groups.

There are many ways to evaluate a selected metabolite profile to assesswhether a subject has or is predisposed to developing CRC and/orcolorectal polyps. The values measured for metabolites can bemathematically combined and the combined value can be correlated to theunderlying diagnostic question. Metabolite values may be combined by anyappropriate mathematical method. Mathematical methods for correlating ametabolite combination to a disease can employ methods such as, but notlimited to, discriminant analysis (DA) (i.e. linear-, quadratic-,regularized-DA), Kernel Methods (i.e. SVM), Nonparametric Methods (i.e.k-Nearest-Neighbor Classifiers), PLS (Partial Least Squares), Tree-BasedMethods (i.e. Logic Regression, CART, Random Forest Methods,Boosting/Bagging Methods), Generalized Linear Models (i.e. LogisticRegression), Principal Components based Methods (i.e. SIMCA),Generalized Additive Models, Fuzzy Logic based Methods, Neural Networksand Genetic Algorithms based Methods. For the SVM model, the linearcoefficients of each feature in an SVM classifier can be used to selectthe most important features. Those features that had the largestabsolute value can be selected, and the SVM model can be re-calculatedusing only the selected features and the training set if necessary.

When comparing test results from two different populations, for example,one with a disease and the other without the disease, a perfectseparation between the two groups is rarely observed. Indeed, thedistribution of the test results will overlap. Therefore, when a cut-offpoint or criterion value to discriminate between the two populations isselected and applied, there will be some cases with the diseasecorrectly classified as positive (True Positive fraction), but somecases with the disease will be classified negative (False Negativefraction). On the other hand, some cases without the disease will becorrectly classified as negative (True Negative fraction), but somecases without the disease will be classified as positive (False Positivefraction).

The diagnostic performance of such a test, or the accuracy of a test todiscriminate diseased groups from healthy groups, can be evaluated usingtools such as ROC curve analysis. The ROC curve is a graphicalrepresentation of the spectrum of sensitivities and specificitiesgenerated using the various cut-offs, using the sensitivity as they-axis and 1-specificity as the x-axis. In an ROC curve the truepositive rate (Sensitivity) is plotted in function of the FP rate(100-Specificity) for different cut-off points. Each point on the ROCcurve represents a sensitivity/specificity pair corresponding to aparticular decision threshold. A test with perfect discrimination (nooverlap in the two distributions) has a ROC curve that passes throughthe upper left corner (100% sensitivity, 100% specificity). Therefore,qualitatively, the closer the plot is to the upper left corner, thehigher the overall accuracy of the test. Area under the ROC curve (AUC)reflects the accuracy of the test and is displayed on the left lowercorner of the plot. An AUC of 0.9 to 1 represents an excellentdiagnostic test whereas an AUC of 0.8-0.9 represents a good test and anAUC of 0.7 to 0.8 represents a fair test.

Development of Reference Metabolite Profiles

Generally, the more metabolites that are assessed, the more accuratewill be the assessment of CRC and/or colorectal polyps. In exemplaryembodiments, more than 240 metabolites were considered, and 69metabolites were used to assess whether a subject has or is predisposedto developing CRC or colorectal polyps. Indeed, other, or additionalurine metabolites beyond these metabolites identified can be included inthe metabolite profile. However, as noted above, this involves greatereffort and cost. In many instances, a less accurate, specific, ordetailed assessment may be sufficient, particularly if the assessment isonly preliminary in nature, or is to be conducted together with orfollowed by another diagnostic test, such as colonoscopy. Further, atest involving the assessment of fewer metabolites may be more readilyreduced to a simplified kit or test that can be used by a subject athome, or by a medical practitioner at the point of care, without needfor sending a urine sample to a laboratory for analysis.

As explained above, VIP values greater than 1 are considered to reflectmetabolites with the greatest potential for discriminating betweenhealthy and diseased subjects. For the assessment of CRC per se, asdistinct from colorectal polyps of any kind, as detailed in Table 1, thefollowing metabolites, have been shown to exhibit VIP values greaterthan 1.0, presented from highest to lowest VIP value: adipate;3-hydroxybutyrate; creatine; guanidoacetate; dimethylamine;hypoxanthine; benzoate; O-acetylcarnitine; pyruvate; methanol; lactate;creatinine; xylose; 3-indoxylsulfate; trigonelline; taurine; threonine;p-methylhistidine; glucose; and 4-hydroxyphenylacetate.

In an embodiment, the reference metabolic profile is directed toassessing whether a subject has or is predisposed to developing CRC, andincludes measurements of concentrations in a urine sample of at leastany 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or20 metabolites selected from the group consisting of: adipate;3-hydroxybutyrate; creatine; guanidoacetate; dimethylamine;hypoxanthine; benzoate; O-acetylcarnitine; pyruvate; methanol; lactate;creatinine; xylose; 3-indoxylsulfate; trigonelline; taurine; threonine;p-methylhistidine; glucose; and 4-hydroxyphenylacetate.

Generally, if fewer than all 20 of these metabolites are to be used inthe reference metabolite profile, preference will be given to those withthe highest VIP values. As described in Table 2, a profile containingonly the top five metabolites was demonstrated to have acceptablesensitivity and specificity, and fewer may be used to develop anacceptable profile. Thus, in various embodiments, the reference profilefor detecting CRC includes one or more metabolites in a set ofmetabolites selected from the group consisting of:

(i) adipate; 3-hydroxybutyrate; creatine; guanidoacetate; dimethylamine;hypoxanthine; benzoate; O-acetylcarnitine; pyruvate; methanol; lactate;creatinine; xylose; 3-indoxylsulfate; trigonelline; taurine; threonine;p-methylhistidine; glucose; and 4-hydroxyphenylacetate;(ii) adipate; 3-hydroxybutyrate; creatine; guanidoacetate;dimethylamine; hypoxanthine; benzoate; O-acetylcarnitine; pyruvate;methanol; lactate; creatinine; xylose; 3-indoxylsulfate; trigonelline;taurine; threonine; p-methylhistidine; and glucose;(iii) adipate; 3-hydroxybutyrate; creatine; guanidoacetate;dimethylamine; hypoxanthine; benzoate; O-acetylcarnitine; pyruvate;methanol; lactate; creatinine; xylose; 3-indoxylsulfate; trigonelline;taurine; threonine; and p-methylhistidine;(iv) adipate; 3-hydroxybutyrate; creatine; guanidoacetate;dimethylamine; hypoxanthine; benzoate; O-acetylcarnitine; pyruvate;methanol; lactate; creatinine; xylose; 3-indoxylsulfate; trigonelline;taurine; and threonine(v) adipate; 3-hydroxybutyrate; creatine; guanidoacetate; dimethylamine;hypoxanthine; benzoate; O-acetylcarnitine; pyruvate; methanol; lactate;creatinine; xylose; 3-indoxylsulfate; trigonelline; and taurine;(vi) adipate; 3-hydroxybutyrate; creatine; guanidoacetate;dimethylamine; hypoxanthine; benzoate; O-acetylcarnitine; pyruvate;methanol; lactate; creatinine; xylose; 3-indoxylsulfate; andtrigonelline;(vii) adipate; 3-hydroxybutyrate; creatine; guanidoacetate;dimethylamine; hypoxanthine; benzoate; O-acetylcarnitine; pyruvate;methanol; lactate; creatinine; xylose; and 3-indoxylsulfate;(viii) adipate; 3-hydroxybutyrate; creatine; guanidoacetate;dimethylamine; hypoxanthine; benzoate; O-acetylcarnitine; pyruvate;methanol; lactate; creatinine; and xylose;(vix) adipate; 3-hydroxybutyrate; creatine; guanidoacetate;dimethylamine; hypoxanthine; benzoate; O-acetylcarnitine; pyruvate;methanol; lactate; and creatinine;(x) adipate; 3-hydroxybutyrate; creatine; guanidoacetate; dimethylamine;hypoxanthine; benzoate; O-acetylcarnitine; pyruvate; methanol; andlactate;(xi) adipate; 3-hydroxybutyrate; creatine; guanidoacetate;dimethylamine; hypoxanthine; benzoate; O-acetylcarnitine; pyruvate; andmethanol;(xii) adipate; 3-hydroxybutyrate; creatine; guanidoacetate;dimethylamine; hypoxanthine; benzoate; O-acetylcarnitine; and pyruvate;(xiii) adipate; 3-hydroxybutyrate; creatine; guanidoacetate;dimethylamine; hypoxanthine; benzoate; and O-acetylcarnitine;(xiv) adipate; 3-hydroxybutyrate; creatine; guanidoacetate;dimethylamine; hypoxanthine; and benzoate;(xv) adipate; 3-hydroxybutyrate; creatine; guanidoacetate;dimethylamine; and hypoxanthine;(xvi) adipate; 3-hydroxybutyrate; creatine; guanidoacetate; anddimethylamine;(xvii) adipate; 3-hydroxybutyrate; creatine; and guanidoacetate;(xviii) adipate; 3-hydroxybutyrate; and creatine;(xix) adipate and 3-hydroxybutyrate; and(xx) adipate.

In some embodiments of the invention, it is the concentration (e.g.measured in μM) of the urine metabolites that is measured, and a higheror lower concentration of the metabolite in the urine of a test subjectrelative to that in reference metabolite profile (based either on raw ornormalized concentrations) is indicative of CRC.

In some embodiments, an elevated concentration of any one or moremetabolites selected from the group consisting of adipate;3-hydroxybutyrate; creatine; guanidoacetate; dimethylamine; benzoate;O-acetylcarnitine; lactate; xylose; 3-indoxylsulfate; trigonelline;taurine; threonine; p-methylhistidine and 4-hydroxyphenylacetate isindicative that the subject has or is predisposed to developing CRC.

It will be understood that by “elevated” it is meant that theconcentration of a metabolite in the urine of a subject that has or ispredisposed to developing CRC is higher than in the urine of subjectsthat do not have or are not predisposed to CRC. For instance, referringto Table 1, it will be seen that the mean concentration of adipate inthe urine of individuals with CRC was 218.1 μM, much higher than themean concentration of adipate in the urine of “normal” subjects withoutCRC, which was found to be 1.3 μM. Thus, on a comparative basis relativeto healthy subjects, subjects with CRC had elevated adipateconcentrations in their urine.

In some embodiments, a reduced concentration of any one or moremetabolites selected from the group consisting of hypoxanthine;pyruvate; methanol; creatinine and glucose is indicative that thesubject has or is predisposed to developing CRC.

It will be understood that by “reduced” it is meant that theconcentration of a metabolite in the urine of a subject that has or ispredisposed to developing CRC is lower than in the urine of subjectsthat do not have or are not predisposed to CRC. For instance, referringto Table 1, it will be seen that the mean concentration of hypoxanthinein the urine of subjects with CRC was 188.4 μM, lower than the meanconcentration of hypoxanthine in the urine of “normal” subjects withoutCRC, which was found to be 208.4 μM. Thus, on a comparative basisrelative to healthy subjects, subjects with CRC had reduced hypoxanthineconcentrations in their urine.

A reference metabolite profile that is diagnostic of colorectal polypsmay be different than a reference metabolite profile for CRC per se.That is, the reference diagnostic profile may be made up of a differentset of relevant metabolites, and different relative concentrations ofthese metabolites may be relevant.

In certain embodiments, the reference metabolite profile is foradenomatous polyps and includes concentrations of at least any 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 or 17 metabolites selectedfrom the group consisting of: butyrate; serine; methanol; β-alanine;p-methylhistidine; 3-hydroxybutyrate; asparagine; trigonelline;3-hydroxyphenylacetate; histidine; acetone; 2-oxoglutarate; ethanol;adipate; 3-hydroxymandelate; tyrosine and benzoate.

As above, these are metabolites found to have VIP scores of 1.0 or aboveand are listed in descending order in Table 5. As above, acceptablespecificity and sensitivity was demonstrated with a profile based ononly the top five metabolites (Table 6) and fewer may be used. Thus, iffewer than all of the metabolites are included in the referencemetabolite profile, the profile may include one or more metabolites in aset of metabolites selected from the group consisting of:

(i) butyrate; serine; methanol; β-alanine; p-methylhistidine;3-hydroxybutyrate; asparagine; trigonelline; 3-hydroxyphenylacetate;histidine; acetone; 2-oxoglutarate; ethanol; adipate;3-hydroxymandelate; tyrosine and benzoate;

(ii) butyrate; serine; methanol; β-alanine; p-methylhistidine;3-hydroxybutyrate; asparagine; trigonelline; 3-hydroxyphenylacetate;histidine; acetone; 2-oxoglutarate; ethanol; adipate; 3-hydroxymandelateand tyrosine;

(iii) butyrate; serine; methanol; β-alanine; p-methylhistidine;3-hydroxybutyrate; asparagine; trigonelline; 3-hydroxyphenylacetate;histidine; acetone; 2-oxoglutarate; ethanol; adipate and3-hydroxymandelate;

(iv) butyrate; serine; methanol; β-alanine; p-methylhistidine;3-hydroxybutyrate; asparagine; trigonelline; 3-hydroxyphenylacetate;histidine; acetone; 2-oxoglutarate; ethanol and adipate;

(v) butyrate; serine; methanol; β-alanine; p-methylhistidine;3-hydroxybutyrate; asparagine; trigonelline; 3-hydroxyphenylacetate;histidine; acetone; 2-oxoglutarate and ethanol;

(vi) butyrate; serine; methanol; β-alanine; p-methylhistidine;3-hydroxybutyrate; asparagine; trigonelline; 3-hydroxyphenylacetate;histidine; acetone and 2-oxoglutarate;

(vii) butyrate; serine; methanol; β-alanine; p-methylhistidine;3-hydroxybutyrate; asparagine; trigonelline; 3-hydroxyphenylacetate;histidine; and acetone;

(viii) butyrate; serine; methanol; β-alanine; p-methylhistidine;3-hydroxybutyrate; asparagine; trigonelline; 3-hydroxyphenylacetate andhistidine;

(ix) butyrate; serine; methanol; β-alanine; p-methylhistidine;3-hydroxybutyrate; asparagine; trigonelline and 3-hydroxyphenylacetate;

(x) butyrate; serine; methanol; β-alanine; p-methylhistidine;3-hydroxybutyrate; asparagine and trigonelline;

(xi) butyrate; serine; methanol; β-alanine; p-methylhistidine;3-hydroxybutyrate and asparagine;

(xii) butyrate; serine; methanol; β-alanine; p-methylhistidine; and3-hydroxybutyrate;

(xiii) butyrate; serine; methanol; β-alanine and p-methylhistidine;

(xiv) butyrate; serine; methanol and β-alanine;

(xv) butyrate; serine and methanol;

(xvi) butyrate and serine; and

(xvii) butyrate.

In some embodiments, an elevated concentration of any one or moremetabolites selected from the group consisting of p-methylhistidine;3-hydroxybutyrate; asparagine; trigonelline; 3-hydroxyphenylacetate;histidine; acetone; adipate; 3-hydroxymandelate; tyrosine and benzoateis indicative that the subject has or is predisposed to developingadenomatous polyps. As above, “elevated” is relative to a correspondingurine metabolite concentration of healthy subjects.

In some embodiments, a reduced concentration of any one or moremetabolites selected from the group consisting of butyrate; serine;methanol; β-alanine; 2-oxoglutarate and ethanol is indicative that thesubject has or is predisposed to developing adenomatous polyps. Asabove, “reduced” is relative to a corresponding urine metaboliteconcentration of healthy subjects.

Elevated and reduced urine metabolite concentrations for subjects havingadenomatous polyps are shown in Table 5.

In some embodiments, the reference metabolite profile is designed toidentify subjects having or predisposed to colorectal polyps, but notnecessarily to distinguish one type of polyp from another. For instance,the polyp may be adenomatous or hyperplastic, but the referencediagnostic profile does not necessarily distinguish between the two.

In certain embodiments, the reference metabolite profile is forcolorectal polyps that are either adenomatous polyps or hyperplasticpolyps and includes urine concentrations of at least any 1, 2, 3, 4, 5,6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,25 or 26 metabolites selected from the group consisting of: butyrate;serine; asparagine; p-methylhistidine; 3-hydroxybutyrate; methanol;3-hydroxymandelate; tyrosine; trigonelline; β-alanine; histidine;dimethylamine; urea; 1,6-anhydro-β-D-glucose; glucose; ethanol;benzoate; acetone; threonine; 2-hydroxyisobutyrate; creatinine;3-hydroxyphenylacetate; 3-indoxylsulfate; hippurate; ascorbate; and4-hydroxyphenylacetate.

As above, these are metabolites found to have VIP scores of 1.0 or aboveand are listed in descending order (Table 3). As above, acceptablespecificity and sensitivity was demonstrated with a profile based ononly the top five metabolites (Table 4) and fewer may be used. Thus, iffewer than all of the metabolites are included in the referencemetabolite profile, the profile may include one or more metabolites in aset of metabolites selected from the group consisting of:

(i) butyrate; serine; asparagine; p-methylhistidine; 3-hydroxybutyrate;methanol; 3-hydroxymandelate; tyrosine; trigonelline; β-alanine;histidine; dimethylamine; urea; 1,6-anhydro-β-D-glucose; glucose;ethanol; benzoate; acetone; threonine; 2-hydroxyisobutyrate; creatinine;3-hydroxyphenylacetate; 3-indoxylsulfate; hippurate; ascorbate; and4-hydroxyphenylacetate;(ii) butyrate; serine; asparagine; p-methylhistidine; 3-hydroxybutyrate;methanol; 3-hydroxymandelate; tyrosine; trigonelline; β-alanine;histidine; dimethylamine; urea; 1,6-anhydro-β-D-glucose; glucose;ethanol; benzoate; acetone; threonine; 2-hydroxyisobutyrate; creatinine;3-hydroxyphenylacetate; 3-indoxylsulfate; hippurate and ascorbate;(iii) butyrate; serine; asparagine; p-methylhistidine;3-hydroxybutyrate; methanol; 3-hydroxymandelate; tyrosine; trigonelline;β-alanine; histidine; dimethylamine; urea; 1,6-anhydro-β-D-glucose;glucose; ethanol; benzoate; acetone; threonine; 2-hydroxyisobutyrate;creatinine; 3-hydroxyphenylacetate; 3-indoxylsulfate and hippurate;(iv) butyrate; serine; asparagine; p-methylhistidine; 3-hydroxybutyrate;methanol; 3-hydroxymandelate; tyrosine; trigonelline; β-alanine;histidine; dimethylamine; urea; 1,6-anhydro-β-D-glucose; glucose;ethanol; benzoate; acetone; threonine; 2-hydroxyisobutyrate; creatinine;3-hydroxyphenylacetate and 3-indoxylsulfate;(v) butyrate; serine; asparagine; p-methylhistidine; 3-hydroxybutyrate;methanol; 3-hydroxymandelate; tyrosine; trigonelline; β-alanine;histidine; dimethylamine; urea; 1,6-anhydro-β-D-glucose; glucose;ethanol; benzoate; acetone; threonine; 2-hydroxyisobutyrate; creatinineand 3-hydroxyphenylacetate;(vi) butyrate; serine; asparagine; p-methylhistidine; 3-hydroxybutyrate;methanol; 3-hydroxymandelate; tyrosine; trigonelline; β-alanine;histidine; dimethylamine; urea; 1,6-anhydro-β-D-glucose; glucose;ethanol; benzoate; acetone; threonine; 2-hydroxyisobutyrate andcreatinine;(vii) butyrate; serine; asparagine; p-methylhistidine;3-hydroxybutyrate; methanol; 3-hydroxymandelate; tyrosine; trigonelline;β-alanine; histidine; dimethylamine; urea; 1,6-anhydro-β-D-glucose;glucose; ethanol; benzoate; acetone; threonine and 2-hydroxyisobutyrate;(viii) butyrate; serine; asparagine; p-methylhistidine;3-hydroxybutyrate; methanol; 3-hydroxymandelate; tyrosine; trigonelline;β-alanine; histidine; dimethylamine; urea; 1,6-anhydro-β-D-glucose;glucose; ethanol; benzoate; acetone and threonine;(vix) butyrate; serine; asparagine; p-methylhistidine;3-hydroxybutyrate; methanol; 3-hydroxymandelate; tyrosine; trigonelline;β-alanine; histidine; dimethylamine; urea; 1,6-anhydro-β-D-glucose;glucose; ethanol; benzoate and acetone;(x) butyrate; serine; asparagine; p-methylhistidine; 3-hydroxybutyrate;methanol; 3-hydroxymandelate; tyrosine; trigonelline; β-alanine;histidine; dimethylamine; urea; 1,6-anhydro-β-D-glucose; glucose;ethanol and benzoate;(xi) butyrate; serine; asparagine; p-methylhistidine; 3-hydroxybutyrate;methanol; 3-hydroxymandelate; tyrosine; trigonelline; β-alanine;histidine; dimethylamine; urea; 1,6-anhydro-β-D-glucose; glucose andethanol;(xii) butyrate; serine; asparagine; p-methylhistidine;3-hydroxybutyrate; methanol; 3-hydroxymandelate; tyrosine; trigonelline;β-alanine; histidine; dimethylamine; urea; 1,6-anhydro-β-D-glucose andglucose;(xiii) butyrate; serine; asparagine; p-methylhistidine;3-hydroxybutyrate; methanol; 3-hydroxymandelate; tyrosine; trigonelline;β-alanine; histidine; dimethylamine; urea and 1,6-anhydro-β-D-glucose;(xiv) butyrate; serine; asparagine; p-methylhistidine;3-hydroxybutyrate; methanol; 3-hydroxymandelate; tyrosine; trigonelline;β-alanine; histidine; dimethylamine and urea;(xv) butyrate; serine; asparagine; p-methylhistidine; 3-hydroxybutyrate;methanol; 3-hydroxymandelate; tyrosine; trigonelline; β-alanine;histidine and dimethylamine;(xvi) butyrate; serine; asparagine; p-methylhistidine;3-hydroxybutyrate; methanol; 3-hydroxymandelate; tyrosine; trigonelline;β-alanine and histidine;(xvii) butyrate; serine; asparagine; p-methylhistidine;3-hydroxybutyrate; methanol; 3-hydroxymandelate; tyrosine; trigonellineand β-alanine;(xviii) butyrate; serine; asparagine; p-methylhistidine;3-hydroxybutyrate; methanol; 3-hydroxymandelate; tyrosine andtrigonelline;(xix) butyrate; serine; asparagine; p-methylhistidine;3-hydroxybutyrate; methanol; 3-hydroxymandelate and tyrosine;(xx) butyrate; serine; asparagine; p-methylhistidine; 3-hydroxybutyrate;methanol and 3-hydroxymandelate;(xxi) butyrate; serine; asparagine; p-methylhistidine; 3-hydroxybutyrateand methanol;(xxii) butyrate; serine; asparagine; p-methylhistidine and3-hydroxybutyrate;(xxiii) butyrate; serine; asparagine and p-methylhistidine;(xxiv) butyrate; serine and asparagine;(xxv) butyrate and serine; and(xxvi) butyrate.

In some embodiments, an elevated concentration of any one or moremetabolites selected from the group consisting of asparagine;p-methylhistidine; 3-hydroxybutyrate; 3-hydroxymandelate; tyrosine;trigonelline; histidine; dimethylamine; urea; 1,6-anhydro-β-D glucose;glucose; benzoate; acetone; threonine; 2-hydroxyisobutyrate; creatinine;3-hydroxyphenylacetate; 3-indoxylsulfate; hippurate; and4-hydroxyphenylacetate is indicative that the subject has or ispredisposed to developing colorectal polyps which are either adenomatouspolyps or hyperplastic polyps. As above, “elevated” is relative to acorresponding urine metabolite concentration of healthy individuals.

In some embodiments, a reduced concentration of any one or moremetabolites selected from the group consisting of butyrate; serine;methanol; β-alanine; ethanol and ascorbate is indicative that thesubject has or is predisposed to developing colorectal polyps which areeither adenomatous polyps or hyperplastic polyps. As above, “reduced” isrelative to a corresponding urine metabolite concentration of healthysubjects.

Elevated and reduced urine metabolite concentrations for subjects havingpolyps that are either adenomatous or hyperplastic are shown in Table 3.

Assessing Whether a Subject has or is Predisposed to Developing CRCand/or Colorectal Polyps

The invention provides methods for assessing whether a subject has or ispredisposed to developing CRC and/or colorectal polyps, the methodcomprising: (a) providing a urine sample from said subject; (b)obtaining a metabolite profile from said urine sample; (c) comparingsaid metabolite profile with a reference metabolite profile; and (d)assessing, based on said comparison in step (c), whether said subjecthas or is predisposed to developing CRC and/or colorectal polyps.

Urine samples can be obtained as described above. The metabolite profilefrom the subject contains the corresponding information concerning thesubject's urine sample as contained in the selected reference metaboliteprofile, as described above. Comparison of the metabolite profile fromthe subject to the reference metabolite profile allows for assessment ofwhether the subject has or is predisposed to developing CRC and/orcolorectal polyps.

Merely by way of an illustrative example, the method might be a methodfor assessing whether a subject has or is predisposed to developing CRC.A urine sample could be taken and concentrations of the followingmetabolites measured: adipate; 3-hydroxybutyrate; creatine;guanidoacetate; dimethylamine; hypoxanthine; benzoate;O-acetylcarnitine; pyruvate; methanol; lactate; creatinine; xylose;3-indoxylsulfate; trigonelline; taurine; threonine; p-methylhistidine;glucose; and 4-hydroxyphenylacetate. The concentration of each of thesemetabolites in the subject's urine is then compared to theconcentrations of the corresponding metabolites in the referencemetabolite profile. Detection of a higher concentration of any one ormore of adipate, 3-hydroxybutyrate, creatine, guanidoacetate,dimethylamine, benzoate, O-acetylcarnitine, lactate, xylose,3-indoxylsulfate, trigonelline, taurine, threonine, p-methylhistidineand 4-hydroxyphenylacetate in the subject's metabolite profile than inthe reference metabolite profile may indicate that the subject has or ispredisposed to developing CRC. Similarly, a lower concentration of anyone or more of hypoxanthine, pyruvate, methanol, creatinine, and glucosein the subject's metabolite profile than in the reference metaboliteprofile may indicate that the subject has or is predisposed todeveloping CRC.

Diagnostic Kits

The invention also provides kits for assessing whether a subject has oris predisposed to developing CRC and/or colorectal polyps. Such kits maycomprise one or more reagents for detecting the presence and/orconcentration of one or more metabolites in a urine sample of a subject,and may include instructions for use of the kit for assessing whether asubject has or is predisposed to developing CRC and/or colorectalpolyps.

The most reliable results are likely obtained when urine samples areprocessed, e.g. by NMR spectroscopy, in a laboratory setting. Forinstance, a urine sample might be obtained from a subject in the officeof a medical practitioner and then sent to a hospital or commercialmedical laboratory for further testing. However, in many instances, itmay be desirable to provide immediate results in a clinician's office orto permit a subject to conduct testing at home. The need for a test thatis portable, pre-packaged, disposable, usable by a subject withoutassistance or direction, etc. may in some instances be of moreimportance than a high degree of accuracy. In many instances,particularly where there will be follow-up with a medical practitioner,a preliminary test, even one with reduced sensitivity and/or specificitymay be sufficient. Thus, an assay presented in kit form may involvedetection and measurement of a relatively small number of metabolites,to reduce the complexity and cost of the assay.

Any form of urine assay capable of detecting urine metabolites asdescribed herein may be used. Typically, the assay will quantitate theurine metabolites to some extent e.g. whether they are higher or lowerin concentration or in amount than a predetermined threshold value. Suchkits may take the form of a test strip, dip stick, cassette, cartridge,chip-based or bead-based array, multi-well plate, or series ofcontainers, or the like. One or more reagents are provided to detect thepresence and/or concentration and/or amount of selected urinemetabolites. The subject's urine may be dispensed directly onto theassay or indirectly from a stored sample. The presence or absence of ametabolite above or below a pre-determined threshold may be displayede.g. by a chromogenic, fluorogenic, electrochemiluminescent or otheroutput, e.g. as in an enzyme immunoassay (EIA) such as an enzyme-linkedimmunoassay (ELISA).

In an embodiment, a kit may comprise a solid substrate, such as e.g. achip, slide, array, etc., with reagents capable of detecting and/orquantitating one or more urine metabolites immobilized at predeterminedlocations on the substrate. By way of an illustrative example, a chipcan be provided with reagents immobilized at discrete, predeterminedlocations for detecting and quantitating in a urine sample theconcentration of adipate; 3-hydroxybutyrate; creatine; guanidoacetateand dimethylamine. As discussed above, elevated levels of thesemetabolites were found in the urine of subjects with CRC. The chip maybe configured such that a detectable output (e.g. colour change) isprovided only if the concentration of one or more of these metabolitesis over a threshold value, the threshold value being selected todistinguish between a metabolite concentration indicative of healthysubjects and those having or predisposed to developing CRC. Thus, thepresence of a detectable output such as a colour change provides animmediate indication that the urine sample contains significantlyelevated levels of one or more relevant urine metabolites, indicatingthat the subject has or is predisposed to developing CRC.

Systems for Performing the Assessment of CRC or Colorectal Polyps

In an embodiment, the invention provides a system for assessing whethera subject has or is predisposed to developing CRC and/or colorectalpolyps. As shown in FIG. 29, such a system may comprise:

(a) a CRC- and/or colorectal polyps-assessing apparatus including acontrol unit and a memory unit to assess a CRC state in a subject; and

(b) an information communication terminal apparatus that provides dataon the presence and/or concentration and/or amount of metabolites in aurine sample from the subject connected to each other communicatively,

wherein the information communication terminal apparatus includes:

(a) a data sending unit that transmits the data on the presence and/orconcentration and/or amount of metabolites in the sample to the CRC-and/or colorectal polyps-assessing apparatus; and

(b) an assessment result-receiving unit that receives the assessmentresult of the CRC and/or colorectal polyps state of the subjecttransmitted from the CRC- and/or colorectal polyps-assessing apparatus,

wherein the control unit of the CRC- and/or colorectal polyps-assessingapparatus includes:

(a) a data-receiving unit that receives the data on the metaboliteconcentration and/or amount of the sample transmitted from theinformation communication terminal apparatus;

(b) a discriminant value-calculating unit that calculates a discriminantvalue that is a value of multivariate discriminant, based on both theconcentration and/or amount value of the metabolite in the samplereceived by the data-receiving unit and a multivariate discriminant withthe concentration and/or amount of the metabolite as explanatoryvariable stored in the memory unit;(c) a discriminant value criterion-assessing unit that assesses the CRCor colorectal polyps state in the subject, based on the discriminantvalue calculated by the discriminant value-calculating unit; and(d) an assessment result-sending unit that transmits the assessmentresult of the subject obtained by the discriminant valuecriterion-assessing unit to the information communication terminalapparatus.Evaluation of Efficacy of Pharmaceutical Agents and/or PhysicalTreatments and/or Surgical Treatment

Metabolomic analysis is ideal for identification of and evaluation ofthe effects of potential pharmaceutical agents and/or new physicaland/or surgical treatments against CRC, colorectal polyps and/oradenomatous polyps. Urine samples can be taken one or more times, bymethods described previously herein, from a subject before and aftertreatment. The treatment can include administration of one or morepharmaceutical agents at one or more doses, and/or carrying out one ormore physical and/or surgical treatments, to or on a subject. Theadministration of pharmaceutical agents can be made in many differentways including, but not limited to, injection, oral administration,patch or ointment application.

The metabolite profiles obtained from the samples can be compared witheach other and/or with the metabolite profile from subjects without CRCand/or colorectal polyps. The comparison can indicate the efficacy ofthe pharmaceutical agents and/or the physical treatment and/or surgicaltreatment through changes of the metabolite profile in urine samples ofthe subject. Also, comorbidities and medications of a subject can bestudied in subsequent analyses to determine their effects on themetabolomic test results and specifically whether they contribute todiscordant results. In addition, the metabolite profiles of the CRCsamples can be correlated with operative and histological findings todetermine whether CRC location or stage can change a metabolite profile.

This invention is further illustrated by the following non-limitingexamples.

Example 1. Assessment of CRC Group Versus Normal Group

Subjects for the normal group were recruited from a population basedstudy of 1,200 asymptomatic subjects who were supposed to be exposed toan average or high risk of CRC, based on family history of colorectalcancer or personal history of colorectal polyps. Subjects for the CRCgroup were all newly diagnosed with CRC.

Four hundred forty four subjects without CRC and/or colorectal polypswere selected and classified as the normal group. Seventy seven CRCsubjects were classified as the CRC group. Clinical information wasobtained from study questionnaires, and subjects completed a medicalquestionnaire, had a FOBT, FIT, and a colonoscopy for determination ofclassification.

Urine samples were collected from subjects of the two groups. The urinesamples were frozen at −80° C. within 24 hours of collection. Urinesample collection containers were pre-filled with sodium azide powder tostop any bacterial growth in the urine while it is waiting to be frozenat −80° C.

Urine samples were thawed at room temperature in the biohood 24 hoursprior to NMR acquisition. For the non-automated (manual) NMRacquisition, 585 μL of each sample was diluted with 65 μL of internalstandard consisting of 5 mM sodium2,2-dimethyl-2-silapentane-5-sulfonate (DSS), 100 mM imidazole and 0.2%sodium azide in 99% D2O (Chenomx Inc., Edmonton, AB) to achieve a totalvolume of 650 μL and stored at 4° C. For the automated (robotic) NMRacquisition, 675 μL of each sample was diluted with 75 μL of the sameChenomx internal standard to achieve a total volume of 750 μL and storedat 4° C. On the day of NMR acquisition, the pH of each sample wasmeasured. Various concentrations of HCl and NaOH were added to thesamples to achieve a pH between 6.7 and 6.8 to minimize chemicalexchange as the chemical shift would change with pH. For the samples forthe non-automated NMR, an aliquot of 600 μL of the samples was placed in5 mm NMR tubes and capped; for the samples for the automated NMR, 700 μLwas used.

Manual Non-Automated Mode:

One-dimensional NMR spectra were acquired using an Oxford 600 Hz NMRspectrometer with a Varian VNMRS two channel console and running VNMRJsoftware version 2.2C on a RHEL 4 host computer in the Canadian NationalHigh Field NMR Centre (NANUC). Samples (600 μL) were set to a depth of66 mm in the depth gage and then inserted into the spectrometer. Allsamples were run at a sweep width (sw) of 7225.43 Hz. The saturationfrequency (sfrq), transmitter offset (tof) and pulse width (pw) were allindividually calibrated at the start of each set of sample runs. The tofranged from (−213 to −215 Hz) and the pw ranged from 6 to 8microseconds. Shims were optimized until an acceptable line width valuewas obtained at relative peaks heights of: 50% (<1.0 Hz), 0.55% (<12.0Hz), and 0.11% (<20.0 Hz). During post-processing of the sample, zerofilling was used to increase the actual acquired data points to the nextlargest factor of 2. No weighting functions were applied. The firstincrement of a 2D-1H,1H-NOESY pulse sequence was utilized for theacquisition of 1H-NMR (Hydrogen-1 nuclear magnetic resonance) data andfor suppressing the solvent signal. Experiments contained a 100 msmixing time along with a 990 ms pre-saturation time (˜80 Hz gammaB 1).Spectra were collected at 25° C. through a total of 32 scans over aperiod of 3.5 minutes; a total recycle delay of 5 seconds was also used.

Automated Mode:

Automated runs followed exactly the same experimental parameters used inthe manual mode with the exception of i) use of 700 μL sample and ii) anadditional 30 s of equilibration time in the NMR to allow the sample toequilibrate to 25° C. All sample handling was done with a Varian 768 ASsample handling robot. The first sample of the batch was manuallyshimmed to satisfactory line width values and subsequent samples wereautomatically shimmed. Any spectra that did not meet acceptable lineheight values were discarded and the sample was re-run.

After the spectra were obtained, samples from both manual and automatedmode were removed from NMR tubes with glass Pasteur pipettes andtransferred into eppendorf tubes. The pH of each sample was thenrechecked to ensure that the pH had not shifted a significant amount.Samples were re-stored in the −80° C. freezer.

Once the spectra were acquired, quantification of metabolites was doneusing Chenomx NMRSuite v4.6 software (Chenomx, Inc. Edmonton, Canada),which compared the integral of a known reference signal (in this caseDSS) with signals derived from a library of compounds to determineconcentration relative to the reference signal. The quantification wasdone by one individual and verified by a second individual to optimizeaccuracy.

Over 240 metabolites were considered, and 72 were found to besignificant, that is, the spectral peaks of 72 metabolites in thecompound library were identified in the spectra of the samples:1,6-Anhydro-β-D-glucose, 1-Methylnicotinamide, 2-Hydroxyisobutyrate,2-Oxoglutarate, 3-Aminoisobutyrate, 3-Hydroxybutyrate,3-Hydroxyisovalerate, 3-Hydroxymandelate, 3-Hydroxyphenylacetate,3-Indoxylsulfate, 4-Hydroxyphenylacetate, Acetate, Acetone, Adipate,Alanine, Ascorbate, Asparagine, Benzoate, Betaine, Butyrate, Carnitine,Citrate, Creatine, Creatinin, DSS (Chemical Shape Indicator),Dimethylamine, Ethanol, Formate, Galactose, Glucose, Glutamine,Glycerol, Glycine, Glycolate, Guanidoacetate, Hippurate, Histidine,Hypoxanthine, Ibuprofen, Isoleucine, Lactate, Leucine, Lysine, Mannitol,Methanol, Methylguanidine, N,N-Dimethylglycine, O-Acetylcarnitine,Pantothenate, Propylene glycol, Pyroglutamate, Pyruvate Salicylurate,Serine, Succinate, Sucrose, Tartrate, Taurine, Threonine, Trigonelline,Trimethylamine, Trimethylamine N-oxide, Tyrosine, Uracil, Urea, Valine,Xylose, cis-Aconitate, trans-Aconitate, β-Alanine, I-Methylhistidine,T-Methylhistidine.

Metabolite concentrations were log transformed to normalize theconcentrations. Those metabolites that were not products of normal humanmetabolism, i.e. xenobiotics, such as ibuprofen and salicylurate, wereexcluded. The internal standard DSS was also excluded in the analysis,and 69 metabolites were obtained as a reference metabolite profile.

The metabolite measurements in samples from the CRC group were comparedto metabolite measurements in samples from the normal group. Simca-P+v12.0.1 software (Umetrics, Umea, Sweden) was used to perform themultivariate statistical analyses to identify differences arisingbetween the groups of data sets. These analyses included PLS-DA, andOPLS.

Further data analysis was preformed in order to determine which specificmetabolites were the strongest contributors to the data separationbetween the CRC group and the normal group samples by a VIP plot. Themetabolites identified with a VIP score of greater than 1 were Adipate,3-Hydroxybutyrate, Creatine, Guanidoacetate, Dimethylamine,Hypoxanthine, Benzoate, O-Acetylcarnitine, Pyruvate, Methanol, Lactate,Creatinine, Xylose, 3-Indoxylsulfate, Trigonelline, Taurine, Threonine,F-Methylhistidine, Glucose, 4-Hydroxyphenylacetate. The result issummarized in Table 1 together with the list of 69 metabolites.

The following assessments were performed with two different metaboliteprofiles, one with all the 69 metabolites found to be significant forthe separation of the CRC group and the normal group, and the other with20 metabolites with a VIP value higher than 1.

The VIP plots were generated using SIMCA-P+ to illustrate whichmetabolites contribute the most to the separation between the normal andCRC groups (FIGS. 1 and 2).

Using two-component separation, the OPLS scatter plots shown in FIGS. 3and 4, implemented in SIMCA-P+12, illustrated the normal group as greysquares and the CRC group as black dots. Notwithstanding a degree ofoverlap, the two groups generally appeared on the different (right andleft) sides of the plot.

The 2-dimensional scatter plots of the PLS model were shown in FIGS. 5and 6. In each plot, the normal group were in grey squares and the CRCgroup were in black dots. A similar separation to the OPLS scatter plotsof the normal group and the CRC group could be seen. Even though therewas an overlap between the CRC group and the normal group, the twogroups appear on the different (top and bottom) sides of each plot.

To generate sensitivity and specificity data, the observed versuspredicted data plots were generated for the OPLS models (FIGS. 7 and 8)and arbitrary cut-off points for the predicted value (YPred) were chosenwhere the two groups overlapped (FIGS. 7 and 8). The grey squares,indicating the normal group, to the left of the cut-off were TN andthose that are to the right of the cut-off were the FP. The black dots,indicating CRC group, to the left of the cut-off were false negatives(FN), while those to the right were the true positives (TP). Sensitivityand specificity data were summarized in Table 2.

In Table 2, the model column indicated which metabolites were used toconstruct the model. The term “main model” referred to the modelcontaining all 69 metabolites. The cut-off column corresponded tocertain cut-off points on the ROC curve. Sensitivity and Specificity aremeasures of how accurate and precise the test is. The ROC Curve is ameasure of how robust the models are. R²Y and Q² are measures of thequality of the models constructed; which means, the higher the numbersthe better the model. A negative number means that the model isunusable.

From Table 2, it could be seen that with a cut-off point ranging from0.114184-0.302331, results in a sensitivity range of 87.18-25.64% andspecificity range of 54.03-98.10% would be achieved when using themetabolites with a VIP score greater than 1. Similarly, differentcut-off points can be used for numerous subsets of the metabolites,which can also be observed in Table 2 with the different subsets ofmetabolites. For example, when using the top 15 metabolites and acut-off range from 0.120717-0.326168 a sensitivity range of 79.49-20.51%and a specificity range of 34.12-99.53% can be achieved.

With the data from Table 2, the ROC curves of sensitivity versus1-specificity were plotted (FIGS. 9 and 10) using STATA10.0 (CollegeStation, Tex.). The ROC curves in the Figures had AUC scores of 0.9178and 0.8465, respectively. This result showed that the metabolite profileconsisting of 20 metabolites out of 69, with higher VIP value than 1,can also be used to assess whether a subject has or is predisposed todeveloping CRC, though the metabolite profile consisting of 69metabolites might provide more accurate assessment. Table 2 alsodemonstrates that even five metabolites with highest VIP values could beused to assess whether a subject has or is predisposed to developingCRC.

Example 2. Assessment of Polyp Group Versus Normal Group

Subjects for the normal group and the polyp group were recruited from apopulation based study of 1,200 asymptomatic subjects who were supposedto be exposed to an average or high risk of CRC, based on family historyof CRC or personal history of colorectal polyps. All subjects completeda medical questionnaire, had a FOBT, FIT, and a colonoscopy to determineclassification of the subjects. One subject in the polyp group was foundto be with CRC, and excluded from the test.

Four hundred forty four subjects without CRC and/or colorectal polypswere selected and classified as the normal group. The polyp groupconsisted of two hundred thirty six with tubular, tubulovillous, villousadenomas and hyperplastic polyps.

The process as described previously in “Assessment of Cancer Groupversus Normal Group” was followed for urine sample collection, treatmentof the sample, NMR acquisition, and analysis of the data obtained.

Over 240 metabolites were considered, and 72 were found to besignificant, that is, the spectral peaks of 72 metabolites in thecompound library were identified in the spectra of the study samples:1,6-Anhydro-β-D-glucose, 1-Methylnicotinamide, 2-Hydroxyisobutyrate,2-Oxoglutarate, 3-Aminoisobutyrate, 3-Hydroxybutyrate,3-Hydroxyisovalerate, 3-Hydroxymandelate, 3-Hydroxyphenylacetate,3-Indoxylsulfate, 4-Hydroxyphenylacetate, Acetate, Acetone, Adipate,Alanine, Ascorbate, Asparagine, Benzoate, Betaine, Butyrate, Carnitine,Citrate, Creatine, Creatinin, DSS (Chemical Shape Indicator),Dimethylamine, Ethanol, Formate, Galactose, Glucose, Glutamine,Glycerol, Glycine, Glycolate, Guanidoacetate, Hippurate, Histidine,Hypoxanthine, Ibuprofen, Isoleucine, Lactate, Leucine, Lysine, Mannitol,Methanol, Methylguanidine, N,N-Dimethylglycine, O-Acetylcarnitine,Pantothenate, Propylene glycol, Pyroglutamate, Pyruvate Salicylurate,Serine, Succinate, Sucrose, Tartrate, Taurine, Threonine, Trigonelline,Trimethylamine, Trimethylamine N-oxide, Tyrosine, Uracil, Urea, Valine,Xylose, cis-Aconitate, trans-Aconitate, β-Alanine, H-Methylhistidine,T-Methylhistidine.

Metabolite concentrations were log transformed to normalize theconcentrations. Those metabolites that were not products of normal humanmetabolism, i.e. xenobiotics, such as ibuprofen and salicylurate, wereexcluded. The internal standard DSS was also excluded in the analysis,and 69 metabolites were obtained as a reference metabolite profile.

The metabolites identified with a VIP score of greater than 1 areButyrate; Serine; Asparagine; p-Methylhistidine; 3-Hydroxybutyrate;Methanol; 3-Hydroxymandelate; Tyrosine; Trigonelline; β-Alanine;Histidine; Dimethylamine; Urea; 1,6-Anhydro-β-D-glucose; Glucose;Ethanol; Benzoate; Acetone; Threonine; 2-Hydroxyisobutyrate; Creatinine;3-Hydroxyphenylacetate; 3-Indoxylsulfate; Hippurate; Ascorbate; and4-Hydroxyphenylacetate. The result was summarized in Table 3 togetherwith the list of 69 metabolites.

The following analysis was performed with two different metaboliteprofiles, one with all the 69 metabolites found to be significant forthe separation of the polyp group and the normal group, and the otherwith 26 metabolites with a VIP value higher than 1.

The VIP plots were generated to illustrate which metabolites contributethe most to the separation between the normal and polyp groups (FIGS. 11and 12). The resulting OPLS (FIGS. 13 and 14), PLS-DA 2-dimensionalscatter plots (FIGS. 15 and 16), observed verses predicted plots (FIGS.17 and 18), ROC curves (FIGS. 19 and 20) and sensitivity & specificitydata (Table 4) were produced.

In the OPLS scatter plot, the normal group was in grey squares and thepolyp group was in black diamonds. FIGS. 13 and 14 showed, even thoughthere was an overlap between the two groups, that the polyp groupclustered together and the normal group also clustered together, andthey appeared on the different (right and left) sides of each plot.

In the PLS-DA scatter plot, the normal group was in grey squares and thepolyp group was in black diamonds. FIGS. 15 and 16 showed, even thoughthere was an overlap between the two groups, similarly to the OPLSscatter plot, the polyp group clustered together on the top of the plotand the normal group clustered together on the bottom.

From Table 4, a sensitivity range of 94-57% and specificity range of40-78% would be achieved with a cut-off range of 0.25-0.45. In thesetting of a screening test, a low FN rate is more important than a lowFP rate, hence higher sensitivity could be achieved at the expense of alower specificity. In this case, a cut-off of 0.3 could be used toachieve a sensitivity of 88% and a specificity of 51%. In contrast,preliminary analysis of fifty-two subjects of the normal and the polypgroup samples that showed FOBT had a sensitivity of 9% and specificityof 100%.

The ROC curves in FIGS. 19 and 20 had the AUC scores of 0.7673 and0.7015, respectively. This result showed that the metabolite profileconsisting of 26 metabolites out of 69, with higher VIP value than 1,can also be used to assess whether a subject has colorectal polyps,though the metabolite profile consisting of 69 metabolites might providemore accurate assessment. Table 4 also demonstrates that even fivemetabolites with highest VIP values could be used to assess whether asubject has or is predisposed to developing colorectal polyps.

Example 3. Assessment of Adenoma Polyp Group Versus Normal Group

Subjects for the normal group and the adenoma group were recruited froma population based study of 1,200 asymptomatic subjects who weresupposed to be exposed to an average or high risk of CRC, based onfamily history of CRC or personal history of colorectal polyps.

Four hundred forty four healthy subjects without CRC and/or colorectalpolyps were selected and classified as the normal group. The adenomagroup consisted of one hundred sixty two subjects with adenomatouspolyp. Clinical information was obtained from study questionnaires, andsubjects completed a medical questionnaire, had a FOBT, FIT, and acolonoscopy for determination of classification.

The process as described previously in “Assessment of Cancer Groupversus Normal Group” was followed for urine sample collection, treatmentof the sample, NMR acquisition, and analysis of the data obtained.

Over 240 metabolites were considered, and 72 were found to besignificant, that is, the spectral peaks of 72 metabolites in thecompound library were identified in the spectra of the study samples:1,6-Anhydro-β-D-glucose, 1-Methylnicotinamide, 2-Hydroxyisobutyrate,2-Oxoglutarate, 3-Aminoisobutyrate, 3-Hydroxybutyrate,3-Hydroxyisovalerate, 3-Hydroxymandelate, 3-Hydroxyphenylacetate,3-Indoxylsulfate, 4-Hydroxyphenylacetate, Acetate, Acetone, Adipate,Alanine, Ascorbate, Asparagine, Benzoate, Betaine, Butyrate, Carnitine,Citrate, Creatine, Creatinin, DSS (Chemical Shape Indicator),Dimethylamine, Ethanol, Formate, Galactose, Glucose, Glutamine,Glycerol, Glycine, Glycolate, Guanidoacetate, Hippurate, Histidine,Hypoxanthine, Ibuprofen, Isoleucine, Lactate, Leucine, Lysine, Mannitol,Methanol, Methylguanidine, N,N-Dimethylglycine, O-Acetylcarnitine,Pantothenate, Propylene glycol, Pyroglutamate, Pyruvate Salicylurate,Serine, Succinate, Sucrose, Tartrate, Taurine, Threonine, Trigonelline,Trimethylamine, Trimethylamine N-oxide, Tyrosine, Uracil, Urea, Valine,Xylose, cis-Aconitate, trans-Aconitate, β-Alanine, H-Methylhistidine,T-Methylhistidine.

Metabolite concentrations were log transformed to normalize theconcentrations. Those metabolites that were not products of normal humanmetabolism, i.e. xenobiotics, such as ibuprofen and salicylurate, wereexcluded. The internal standard DSS was also excluded in the analysis,and 69 metabolites were obtained as a reference metabolite profile.

The metabolites identified with a VIP score of greater than one areButyrate, Serine, Asparagine, H-Methylhistidine, 3-Hydroxybutyrate,Methanol, 3-Hydroxymandelate, Tyrosine, Trigonelline, β-Alanine,Histidine, Dimethylamine, Urea, 1-6-Anhydro-β-D-glucose, Glucose,Ethanol, Benzoate, Acetone, Threonine, 2-Hydroxyisobutyrate, Creatinine,3-Hydroxy phenylacetate, 3-Indoxylsulfate, hippurate, Ascorbate,4-Hydroxyphenylacetate. The result was summarized in Table 5 togetherwith the list of 69 metabolites.

The following analysis was performed with two different metaboliteprofiles, one with all the 69 important metabolites, and the other with17 metabolites with a VIP value higher than 1.

The VIP plots were generated to illustrate which metabolites contributethe most to the separation between the normal and adenoma groups (FIGS.21 and 22). The resulting OPLS (FIG. 23), PLS scatter plots (not shown),observed vs. predicted plots (FIGS. 24 and 25), ROC curve (FIGS. 26 and27), and sensitivity & specificity data (Table 6) were produced.

In the OPLS scatter plot, the normal group is in grey squares and thepolyp group is in black diamonds. FIG. 23 shows, even though there is anoverlap between the two groups, that the polyp group clusters togetherand the normal group also clusters together, and they appear on thedifferent (right and left) sides of the plot. The OPLS scatter plot for17 metabolites with a VIP value higher than 1 is not shown.

In the PLS-DA scatter plot, the normal group is in grey squares and thepolyp group is in black diamonds. Even though there is an overlapbetween the two groups, similarly to the OPLS scatter plot, the polypgroup clusters together on the top of the plot and the normal groupclusters together on the bottom.

From Table 6, a sensitivity range of 65.55-5.88% and specificity rangeof 50.71-98.58% would be achieved with a cut-off range of0.329791-0.577397 for the metabolites with a VIP score greater than 1.In the setting of a screening test, a low FN rate is more important thana low FP rate, hence higher sensitivity could be achieved at the expenseof a lower specificity. In this case, a cut-off of 0.329791 could beused to achieve a sensitivity of 65.55% and a specificity of 50.71%. Incontrast, preliminary analysis of fifty-two normal and colorectal polypssamples that showed FOBT had a sensitivity of 9% and specificity of100%.

The ROC curves in FIGS. 26 and 27 had the AUC scores of 0.7524 and0.6937, respectively. This result showed that the metabolite profileconsisting of 17 metabolites out of 69, with higher VIP value than 1,can also be used to assess whether a subject has adenomatous polyps,though the metabolite profile consisting of 69 metabolites might providemore accurate assessment. Table 6 also demonstrates that even fivemetabolites with highest VIP values could be used to assess whether asubject has or is predisposed to developing adenomatous polyps.

Example 4. Assessment of Adenoma Polyp Group Versus Hyperplastic PolypGroup

A total of 110 urine samples from subjects with hyperplastic polyps wereintroduced blindly to the Normal versus Adenoma model discussed inExample 3. The analysis result showed that the metabolite profile ofhyperplastic polyps was more alike with the adenomatous group's than thenormal group's (FIG. 29). This was further confirmed by an attempt toestablish an OPLS model between hyperplastic polyps and adenomatouspolyps. A meaningful model to separate the two groups could not beconstructed (R²Y=0.126, Q²=−0.0771).

This result suggests that some of the hyperplastic polyps might bepre-cancerous like the adenomatous polyps and thus display aprecancerous metabolomic fingerprint.

Example 5. Analytical Methods and their Application

Analytical Methods

PLS (Conventional): Conventional PLS applies to the two-block (X/Y)regression problem. It uses X to construct a model of Y, where theobjective is to predict the latter from the former for new samples inthe prediction set. In that sense, PLS is unidirectional, i.e., X→Y, butnot vice versa.

When X is composed of e.g. spectroscopic data, process readings ormeasurements from bioanalytical platforms, there is a risk thatsystematic variation may reside in X which is not linearly correlatedwith Y. Such variability in X is usually called Y-orthogonal variation.Although Y-orthogonal variation in X does not affect the predictivepower of a PLS model, it may negatively affect model interpretation. Thescore-loading correspondence is perturbed by the presence ofY-orthogonal variation in X.

OPLS: The OPLS method is a recent modification of the PLS method, whichis designed to handle variation in X that is orthogonal to Y. It is anextension to the supervised PLS regression method with an integratedOrthogonal signal correction (OSC) filter, which removes theuncorrelated signals resulting in information of the within-classvariation. OPLS separates the systematic variation in X into two parts,one that is linearly related (and therefore predictive) to Y and onethat is orthogonal to Y. The predictive variation of Y in X is modeledby the predictive components. The variation in X which is orthogonal toY is modeled by the orthogonal components. This partitioning of theX-data provides improved model transparency and interpretability, butdoes not change the predictive power. Similarly to PLS, OPLS is aunidirectional method, where the scope is the relation X→Y.

OPLS Scatter Plot:

The scatter plot is of the OPLS model.

O2PLS: O2PLS is a generalization of OPLS. In contrast to PLS and OPLS,O2PLS is bidirectional, i.e. X←→Y, and therefore X can be used topredict Y, and Y can be used to predict X. Additionally, with O2PLS itis possible to partition the systematic variability in X and Y intothree parts, (i) the X/Y joint predictive variation, (ii) theY-orthogonal variation in X, and (iii) the X-unrelated variation in Y.

FIG. 30 is an overview of the O2PLS model relating two data tables toeach other. The Y-orthogonal variation in X (left-hand side of theFigure) represents the variation of the observations in X that isvarying orthogonally to the corresponding structure in Y. This variationis unique to X. The X/Y joint predictive variation (middle part of theFigure) describes the predictive variation between X and Y, theinformation overlap. The X-unrelated variation in Y (right-hand side ofthe Figure) corresponds to the variation of the observations in Y thatis varying orthogonally to the corresponding structure in X. Thisvariation is unique to Y.

The ability to interpret the X/Y joint predictive variation separatedfrom the non-correlated variation implies that the model interpretationis refined and simplified. Furthermore, it should be noted that for thesingle-y case the OPLS and O2PLS methods are identical. For such a modelthere can only be one predictive component expressing the joint X/Ypredictive variation.

PLS-DA Scatter Plot:

This scatter plot is of the partial least squares discriminant analysis(PLS-DA) model. Conventional PLS is used where a quantitativerelationship exists between two data tables X & Y; it uses X toconstruct a model of Y, where the objective is to predict Y from the Xfor new samples in the prediction set. It is another statistical methodused to compress multidimensional and complex data sets into a moremanageable dataset.

Observed vs. Predicted Plot:

The observed vs. predicted plot displays the observed values vs. thefitted or predicted values for the selected response. The observed vs.predicted plot is a scatter plot of the Y variables (which are normalvs. cancer, adenoma, or polyps) verses the predicted values. Theobserved vs. predicted plot provides with Y predicted values, asassigned by the model, for each sample along with their observed (normalor cancer/adenoma/polyp) value. Then, these values are taken to generatea ROC curve. The observed vs. predicted plot also allows to determinethe true positives, false positives, true negatives, and falsenegatives, to calculate sensitivity and specificity with a range ofcut-offs, and to view the overlap present between two groups.

ROC Curve:

The receiver operating characteristic (ROC) Curve is a graphicalrepresentation of the spectrum of sensitivities and specificitiesgenerated using the various cut-offs, using the sensitivity as they-axis and 1-specificity as the x-axis. Area under the ROC curve (AUC)reflects the accuracy of the test and is displayed on the left lowercorner of the plot. An AUC of 0.9 to 1 represents an excellentdiagnostic test whereas an AUC of 0.8-0.9 represents a good test and anAUC of 0.7 to 0.8 represents a fair test.

VIP Plot:

Variable Importance in the Projection (VIP) plot allows to identifywhich metabolites have a greater impact on driving the separationbetween groups in models. Each metabolite used to construct models isassigned a VIP score; this score is assigned through a statisticalformula that is used to calculate the influence of each model. Thehigher the VIP score, the greater the influence of the metabolite withthe score on shaping the model. VIP also allows for the comparison ofone metabolite to another. Terms with a large VIP (greater then 1) aresaid to be the most relevant for explaining ‘Y’.

Analytical Methods Used

OPLS and PLS-DA Scatter Plot:

The orthogonal PLS named O2PLS has been implemented in SIMCA-P+ 12.O2PLS is bidirectional, i.e. X←→Y, and therefore X can be used topredict Y, and Y can be used to predict X. For the single-y case theOPLS and O2PLS methods are identical.

The O2PLS model can be written as:X=T _(P) P′ _(P) +T _(O) P′ _(O) +E (for model of X)  (1)Y=U _(P) Q′ _(P) +U _(O) Q′ _(O) +F (for model of Y)  (2)

where a linear relationship exists between T_(P) and U_(P). Here, thescore vectors in T_(P) and T_(O) are mutually orthogonal. The number ofcomponents in the respective set of components is determined using crossvalidation.

For any part of the OPLS/O2PLS model, the percentages explained andpredicted variances can be obtained from plots and lists in thesoftware. The vectors listed in Table 7 are unique for OPLS/O2PLS. Thesevectors in addition to the ones listed for PLS are computed for eachcomponent.

ROC Curve (Receiver Operating Characteristic): ROC curves were generatedusing STATA 10.0 (College Station, Tex.), along with the ROC curves acomplete sensitivity and specificity report was also generated. The ROCcurve is a fundamental tool for diagnostic test evaluation. In a ROCcurve the true positive rate (Sensitivity) is plotted in function of thefalse positive rate (100-Specificity) for different cut-off points of aparameter. Each point on the ROC curve represents asensitivity/specificity pair corresponding to a particular decisionthreshold. The area under the ROC curve is a measure of how well aparameter can distinguish between two diagnostic groups(diseased/normal).

The diagnostic performance of a test, or the accuracy of a test todiscriminate diseased cases from normal cases is evaluated usingReceiver Operating Characteristic (ROC) curve analysis. ROC curves canalso be used to compare the diagnostic performance of two or morelaboratory or diagnostic tests.

A test result comparing two populations, for example, one with a diseaseand the other without the disease, a perfect separation between the twogroups is rarely observed. Indeed, the distribution of the test resultswill overlap, as shown in the following figure. Therefore, when acut-off point or criterion value to discriminate between the twopopulations is selected and applied, there will be some cases with thedisease correctly classified as positive (TP=True Positive fraction),but some cases with the disease will be classified negative (FN=FalseNegative fraction). On the other hand, some cases without the diseasewill be correctly classified as negative (TN=True Negative fraction),but some cases without the disease will be classified as positive(FP=False Positive fraction). In a Receiver Operating Characteristic(ROC) curve the true positive rate (Sensitivity) is plotted in functionof the false positive rate (100-Specificity) for different cut-offpoints. Each point on the ROC curve represents a sensitivity/specificitypair corresponding to a particular decision threshold. A test withperfect discrimination (no overlap in the two distributions) has a ROCcurve that passes through the upper left corner (100% sensitivity, 100%specificity). Therefore the closer the ROC curve is to the upper leftcorner, the higher the overall accuracy of the test.

VIP Plot:

SIMCA-P+ computes the influence on Y of every term (xk) in the model,called VIP (variable importance in the projection). VIP is the sum overall model dimensions of the contributions VIN (variable influence). Fora given PLS dimension, a, (VIN)_(ak) ² is equal to the squared PLSweight (w_(ak))² of that term, multiplied by the explained SS of thatPLS dimension. The accumulated (over all PLS dimensions) value is:VIP_(ak) ²=Σ(VIN)_(k) ²

where the summation is made over a=1 to A. This value is then divided bythe total explained SS by the PLS model and multiplied by the number ofterms in the model. The final VIP is the square root of that number. Theformula can also be expressed as:

${VIP}_{Ak} = \sqrt{\sum\limits_{a = 1}^{A}{( {w_{ak}^{2}*( {{SSY}_{a - I} - {SSY}_{a}} )} )*\frac{K}{( {{SSY}_{a} - {SSY}_{A}} )}}}$

The Sum of squares of all VIP's is equal to the number of terms in themodel hence the average VIP is equal to 1. One can compare the VIP ofone term to the others. Terms with large VIP, larger than 1, are themost relevant for explaining Y. The VIP plot shows which are the mostimportant variables over the model as a whole.

The VIP plot carries similar information to the coefficients plot and inpractical terms the two plots often look very similar. The majordifference is that the VIP plot describes which X variables characterizethe X block well AND which variables correlate with Y. PLS is a dualtechnique which tries to finds directions in X which both characterize Xwell and are related to Y. In extreme cases, it is possible for an Xvariable to have a high VIP but not be related to Y at all.

The VIP values summarize the overall contribution of each X-variable tothe PLS model, summed over all components and weighted according to theY variation accounted for by each component, therefore you only ever getone VIP plot per model.

Support Vector Machines (SVM): Classifiers were built using SupportVector Machines (SVM). SVMs separate the Polyp vs Normal data points inn-dimensional space (where n is the number of features) such that themargin of separation is maximized. We built a linear SVM, which meansthat a linear equation is created:prediction(x)=w ₁ *x ₁ +w ₂ *x ₂ + . . . +w _(n) *x _(n) −b

The xi values are the individual values of the feature vector for asubject (as described in the “Classification” section). The wi valuesare the weight values that are found by the SVM algorithm, along withthe b parameter that helps fit the equation to the data set.

TABLE 1 VIP scores (Normal group vs. CRC group) with concentrationanalysis (concentrations in μM) Normals Cancer Higher in Higher in VarID (Primary) VIP score min max mean median min max mean median NormalCancer Adipate 3.93 0.0 103.9 1.3 0.0 0.0 8645.5 218.1 0.0 x3-Hydroxybutyrate 2.25 0.0 498.4 11.7 0.0 0.0 3075.7 157.0 0.0 xCreatine 1.96 0.0 15102.4 2099.7 1563.5 0.0 13477.6 2280.7 1339.0 xGuanidoacetate 1.95 0.0 1781.0 204.0 143.0 0.0 2857.9 232.0 148.9 xDimethylamine 1.82 193.0 24617.4 5643.3 4234.9 716.0 35527.5 8175.96212.0 x Hypoxanthine 1.66 0.0 2108.5 208.4 106.5 0.0 1240.1 188.4 144.1x Benzoate 1.64 0.0 567.3 3.5 0.0 0.0 1130.9 35.0 0.0 xO-Acetylcarnitine 1.60 0.0 131.3 24.7 17.5 0.0 168.2 30.0 21.3 xPyruvate 1.56 0.0 539.8 35.4 10.0 0.0 341.2 28.4 8.0 x Methanol 1.52 0.04738.5 224.5 0.0 0.0 2783.6 215.9 0.0 x Lactate 1.28 0.0 31.5 4.1 0.00.0 90.0 8.2 0.0 x Creatinine 1.26 0.0 10201.1 331.0 58.1 0.0 1245.5109.8 0.0 x Xylose 1.22 7.1 8301.4 308.6 163.1 9.9 1554.7 364.0 237.0 x3-Indoxylsulfate 1.19 0.0 1317.6 120.5 82.5 0.0 1207.0 209.1 135.5 xTrigonelline 1.13 0.0 474.7 78.5 48.7 0.0 450.6 99.6 60.2 x Taurine 1.060.0 536.6 39.0 22.5 0.0 416.3 43.3 18.7 x Threonine 1.04 0.0 888.3 45.513.4 0.0 715.5 79.1 35.0 x p-Methylhistidine 1.04 0.0 113.8 20.3 14.20.0 164.9 25.7 18.0 x Glucose 1.03 0.0 614.8 12.8 0.0 0.0 460.6 7.4 0.0x 4-Hydroxyphenylacetate 1.01 0.0 1401.1 72.6 48.8 0.0 856.0 102.7 57.9x 1,6-Anhydro-Î²-D 0.98 0.0 2763.6 35.7 13.8 0.0 140.4 27.8 18.1 xglucose Sucrose 0.91 0.0 982.2 87.7 0.0 0.0 1419.5 96.3 0.0 x β-Alanine0.87 6976.6 441697.0 127007.5 111896.6 8573.4 324813.3 115212.8 99859.9x Formate 0.86 0.0 27789.2 250.7 0.0 0.0 261.1 9.7 0.0 x3-Hydroxymandelate 0.81 0.0 2539.3 60.0 0.0 0.0 750.9 37.4 0.0 xTrimethylamine N-oxide 0.78 0.0 5028.3 283.2 132.2 0.0 2465.1 450.2283.1 x Carnitine 0.76 0.0 907.1 47.8 22.7 0.0 972.1 85.5 36.4 xIsoleucine 0.76 0.0 1022.5 21.4 9.3 0.0 401.7 55.4 17.8 x Valine 0.720.0 66.4 9.5 6.5 0.0 217.1 12.8 5.4 x Pantothenate 0.69 0.0 321.3 20.311.6 0.0 752.2 57.6 19.5 x Galactose 0.66 5.1 772.6 121.1 96.0 13.83227.7 207.6 105.8 x 3-Hydroxyphenylacetate 0.66 0.0 188.6 11.9 0.0 0.0249.2 10.7 0.0 x Succinate 0.62 0.0 282.0 17.9 10.7 0.0 481.1 34.8 19.4x Citrate 0.58 0.0 864.8 140.3 79.4 0.0 1071.5 200.4 108.6 x Leucine0.57 0.0 2897.0 97.8 52.0 3.8 2710.6 208.9 60.8 x Trimethylamine 0.540.0 4024.6 104.7 12.2 0.0 1883.9 119.2 5.7 x 2-Oxoglutarate 0.53 0.01256.7 56.2 27.0 0.0 409.9 53.9 12.8 x N,N-Dimethylglycine 0.52 0.0415.5 29.4 17.3 0.0 188.3 27.7 18.0 x Glycerol 0.51 0.0 2004.7 149.781.6 0.0 1181.5 172.0 98.4 x Lysine 0.47 0.0 112.4 12.6 9.7 0.0 136.917.4 12.2 x 1-Methylnicotinamide 0.44 0.0 603.3 64.5 26.9 0.0 410.6 36.80.0 x Ethanol 0.42 8.2 1494.3 194.3 135.0 21.7 1317.2 329.7 247.2 xAcetate 0.41 0.0 12892.6 85.6 33.1 0.0 8769.3 268.5 45.9 x Ascorbate0.39 0.0 12949.8 276.2 29.8 0.0 4539.5 237.3 0.0 x Tyrosine 0.39 0.0976.3 71.2 48.9 0.0 298.4 64.4 36.4 x t-Methylhistidine 0.38 0.0 3078.977.0 0.0 0.0 2022.0 162.4 61.0 x Urea 0.37 0.0 4771.9 246.5 128.6 0.01125.0 173.9 90.5 x Glycolate 0.35 27.8 4976.9 699.3 506.0 0.0 2767.5736.0 602.0 x cis-Aconitate 0.34 0.0 551.8 62.9 42.6 0.0 236.2 68.8 53.0x Propylene glycol 0.30 0.0 3745.6 227.6 60.4 0.0 5091.3 190.0 0.0 xTartrate 0.28 0.0 442.9 9.3 0.0 0.0 63.4 1.6 0.0 x Pyroglutamate 0.260.0 536.1 21.7 13.2 0.0 195.9 19.9 8.5 x Alanine 0.25 0.0 1431.3 169.3110.5 0.0 786.7 179.6 138.8 x Acetone 0.25 0.0 115.1 10.0 6.8 0.0 1788.457.2 7.7 x Hippurate 0.23 0.0 1057.1 147.3 98.3 0.0 813.4 95.6 53.8 x2-Hydroxyisobutyrate 0.22 0.0 643.1 30.9 21.6 0.0 148.5 33.4 24.8 xSerine 0.21 0.0 917.4 126.6 92.8 0.0 965.2 148.8 99.5 x Histidine 0.2019.0 45262.7 1675.2 862.7 51.2 7274.5 1461.1 849.1 x 3-Aminoisobutyrate0.20 0.0 1605.2 83.4 36.2 0.0 3350.0 160.5 57.5 x Betaine 0.18 0.02675.7 90.9 51.9 0.0 457.9 81.5 51.5 x Glycine 0.18 0.0 1337.0 7.3 0.00.0 0.0 0.0 0.0 x Butyrate 0.14 0.0 96.4 3.0 0.0 0.0 57.4 3.9 0.0 xtrans-Aconitate 0.07 0.0 530.1 12.3 0.0 0.0 351.2 17.1 0.0 x3-Hydroxyisovalerate 0.07 0.0 243.3 31.3 21.9 0.0 140.1 33.3 20.6 xMethylguanidine 0.07 0.0 1054.6 57.3 21.7 0.0 490.8 33.5 17.0 x Uracil0.06 0.0 456.2 29.1 18.4 0.0 238.1 28.3 19.3 x Mannitol 0.06 0.0 1877.443.5 0.0 0.0 1533.8 65.1 0.0 x Asparagine 0.02 0.0 670.6 40.2 0.0 0.0292.0 41.1 0.0 x Glutamine 0.00 0.0 13433.0 293.2 114.4 0.0 1747.8 293.3162.8 x

TABLE 2 Sensitivity and specificity data (Normal group vs. CRC group)Training Set Testing Set Model Cutoff Sensitivity Specificity ROC CurveR2Y Q2 Sensitivity Specificity Main Model  0.0885604 97.40% 50.00%0.9178 0.408 0.333 94.87% 56.40% 0.170391 90.91% 73.22% 76.92% 74.41%0.226651 83.12% 82.94% 64.10% 85.78% 0.412168 50.65% 97.16% 20.51%98.10% Top 15 0.120717 88.31% 57.35% 0.8281 0.231 0.195 79.49% 34.12%0.136656 79.22% 66.59% 74.36% 82.94% 0.148472 71.43% 71.33% 66.67%91.47% 0.326168 37.66% 97.16% 20.51% 99.53% Top 14 0.126112 88.31%59.48% 0.8218 0.226 0.186 84.62% 63.51% 0.133453 81.82% 64.22% 82.05%68.72% 0.153027 74.03% 72.75% 69.23% 79.15% 0.306811 44.16% 97.16%20.15% 98.58% Top 13 0.129639 85.71% 59.48% 0.8117 0.213 0.174 84.62%63.98% 0.14178  79.22% 66.82% 71.79% 71.56% 0.150067 71.43% 71.33%69.23% 75.36% 0.305146 38.96% 97.16% 17.95% 99.05% Top 12 0.12968285.71% 58.77% 0.8069 0.209 0.17 84.62% 64.93% 0.142588 79.22% 66.82%71.79% 72.99% 0.153333 72.73% 72.04% 69.23% 78.20% 0.304388 37.66%97.16% 17.95% 99.53% Top 11 0.132533 85.71% 60.19% 0.8129 0.212 0.17382.05% 65.88% 0.144688 79.22% 68.01% 71.79% 75.36% 0.153709 72.73%72.51% 69.23% 78.20% 0.302045 37.66% 97.16% 17.95% 99.53% Top 100.133508 85.71% 60.43% 0.8143 0.212 0.181 84.62% 67.30% 0.147835 79.22%69.91% 71.79% 74.88% 0.155504 72.73% 72.51% 69.23% 77.73% 0.29876536.36% 97.16% 20.51% 98.58% Top 9 0.131493 85.71% 60.19% 0.805 0.1990.166 79.49% 65.40% 0.138175 77.92% 64.93% 76.92% 70.14% 0.148832 72.73%72.27% 64.10% 76.30% 0.282037 36.36% 97.16% 17.95% 97.63% Top 8 0.13149385.71% 60.43% 0.805 0.196 0.162 84.62% 63.03% 0.144356 77.92% 69.43%71.79% 73.93% 0.149313 71.43% 72.27% 64.10% 75.83% 0.282037 36.36%97.16% 17.95% 98.10% Top 7 0.127899 85.71% 54.74% 0.8033 0.196 0.16982.05% 61.14% 0.141203 77.92% 68.01% 76.92% 74.41% 0.147994 71.43%71.33% 69.23% 76.78% 0.282972 36.36% 97.16% 17.95% 98.58% Top 6 0.10835484.42% 50.00% 0.7653 0.167 0.152 84.62% 56.40% 0.118968 75.32% 57.11%82.05% 63.98% 0.138547 67.53% 67.30% 71.79% 72 99% 0.312037 32.47%97.16% 23.08% 98.10% Top 5 0.117829 84.42% 51.18% 0.7794 0.17 0.16489.74% 56.87% 0.134735 76.62% 63.74% 74.36% 70.14% 0.145389 68.83%68.72% 69.23% 73.93% 0.302779 28.57% 97.16% 20.51% 98.58% VIP > 10.114184 92.21% 50.47% 0.8465 0.25 0.211 87.18% 54.03% 0.132386 83.12%64.22% 76.92% 70.14% 0.152742 75.32% 75.12% 69.23% 78.20% 0.30233148.05% 97.16% 25.64% 98.10% ** Model named VIP > 1 contains 20metabolites

TABLE 3 VIP scores (Normal group vs. Polyp group) with concentrationanalysis (concentrations in μM) Normals Polyps Higher in Higher in VarID (Primary) VIP score min max mean median min max mean median NormalPolyp Butyrate 2.85 0.0 96.4 3.0 0.0 0.0 15.3 0.1 0.0 x Serine 2.70 0.0982.2 87.7 0.0 0.0 851.5 45.7 0.0 x Asparagine 1.73 0.0 670.6 40.2 0.00.0 402.0 47.5 34.5 x p-Methylhistidine 1.65 0.0 3745.6 227.6 60.4 0.02919.3 275.5 118.9 x 3-Hydroxybutyrate 1.65 0.0 498.4 11.7 0.0 0.03392.5 19.1 0.0 x Methanol 1.59 0.0 1054.6 57.3 21.7 0.0 1019.6 39.717.4 x 3-Hydroxy- 1.57 0.0 2539.3 60.0 0.0 0.0 947.6 82.2 0.7 xmandelate Tyrosine 1.52 0.0 551.8 62.9 42.6 0.0 1196.3 80.6 61.2 xTrigonelline 1.51 0.0 4771.9 246.5 128.6 0.0 1789.8 287.8 204.6 xβ-Alanine 1.45 0.0 442.9 9.3 0.0 0.0 189.5 3.1 0.0 x Histidine 1.38 0.02108.5 208.4 106.5 0.0 3400.1 267.0 153.6 x Dimethylamine 1.36 8.21494.3 194.3 135.0 17.3 1146.5 225.3 177.2 x Urea 1.28 6976.6 441697.0127007.5 111896.6 16667.4 376686.7 141754.5 129086.3 x 1,6-Anhydro-Î²-1.25 0.0 603.3 64.5 26.9 0.0 1012.1 80.3 40.1 x D-glucose Glucose 1.220.0 13433.0 293.2 114.4 0.0 63614.4 863.9 130.8 x Ethanol 1.14 0.027789.2 250.7 0.0 0.0 6405.3 88.9 0.0 x Benzoate 1.13 0.0 567.3 3.5 0.00.0 6282.2 33.9 0.0 x Acetone 1.09 0.0 115.1 10.0 6.8 0.0 778.8 11.7 6.6x Threonine 1.06 0.0 976.3 71.2 48.9 0.0 441.7 79.3 60.2 x 2-Hydroxyiso-1.05 0.0 643.1 30.9 21.6 0.0 162.4 33.9 27.3 x butyrate Creatinine 1.04193.0 24617.4 5643.3 4234.9 0.0 31595.9 6528.6 5403.3 x 3-Hydroxy- 1.040.0 188.6 11.9 0.0 0.0 152.3 15.1 0.0 x phenylacetate 3-Indoxylsulfate1.02 0.0 1317.6 120.5 82.5 0.0 585.8 130.3 100.2 x Hippurate 1.02 19.045262.7 1675.2 862.7 0.0 21449.0 1947.0 1078.2 x Ascorbate 1.01 0.012949.8 276.2 29.8 0.0 10663.2 236.8 0.0 x 4-Hydroxy- 1.01 0.0 1401.172.6 48.8 0.0 1354.3 84.8 57.8 x phenylacetate N,N-Dimethyl- 0.95 0.0131.3 24.7 17.5 0.0 387.6 29.2 19.8 x glycine Adipate 0.95 0.0 103.9 1.30.0 0.0 837.7 6.8 0.0 x Alanine 0.95 0.0 1431.3 169.3 110.5 0.0 1621.6185.5 137.9 x Hypoxanthine 0.95 0.0 1022.5 21.4 9.3 0.0 555.6 23.7 14.3x 3-Aminoiso- 0.85 0.0 1605.2 83.4 36.2 0.0 2222.4 89.8 34.5 x butyratecis-Aconitate 0.83 0.0 864.8 140.3 79.4 0.0 1289.9 169.7 105.1 xTrimethylamine 0.80 7.1 8301.4 308.6 163.1 0.0 5752.9 324.8 215.7 xN-oxide 3-Hydroxy- 0.79 0.0 243.3 31.3 21.9 0.0 141.5 32.8 26.9 xisovalerate Mannitol 0.79 0.0 4738.5 224.5 0.0 0.0 6932.3 321.5 0.0 xtrans-Aconitate 0.75 0.0 456.2 29.1 18.4 0.0 515.1 33.1 20.8 x Valine0.72 0.0 113.8 20.3 14.2 0.0 151.2 22.8 18.4 x Trimethylamine 0.62 0.066.4 9.5 6.5 0.0 270.7 11.3 7.5 x t-Methylhistidine 0.61 0.0 474.7 78.548.7 0.0 706.5 92.6 75.8 x Glycine 0.61 27.8 4976.9 699.3 506.0 0.08600.5 815.7 504.6 x Lactate 0.58 0.0 2897.0 97.8 52.0 0.0 3269.3 109.352.7 x Tartrate 0.55 0.0 4024.6 104.7 12.2 0.0 2263.2 104.9 16.3 xO-Acetylcarnitine 0.55 0.0 321.3 20.3 11.6 0.0 349.9 19.1 12.2 xPropylene glycol 0.53 0.0 539.8 35.4 10.0 0.0 594.3 38.5 4.9 x Citrate0.52 0.0 15102.4 2099.7 1563.5 0.0 8519.8 2126.3 1566.6 x Pyruvate 0.510.0 282.0 17.9 10.7 0.0 109.7 19.7 13.0 x Betaine 0.47 0.0 2675.7 90.951.9 0.0 740.3 84.9 59.7 x Taurine 0.47 0.0 5028.3 283.2 132.2 0.02142.7 302.2 182.8 x Pyroglutamate 0.43 0.0 917.4 126.6 92.8 0.0 587.5134.4 111.9 x Creatine 0.38 0.0 10201.1 331.0 58.1 0.0 4663.5 273.1 61.7x Carnitine 0.34 0.0 907.1 47.8 22.7 0.0 359.8 48.1 30.6 xMethylguanidine 0.34 0.0 415.5 29.4 17.3 0.0 250.0 28.7 20.8 xIsoleucine 0.32 0.0 31.5 4.1 0.0 0.0 69.6 4.6 0.0 x Galactose 0.29 0.0614.8 12.8 0.0 0.0 248.0 6.6 0.0 x Formate 0.29 5.1 772.6 121.1 96.0 0.01424.0 128.3 101.4 x Uracil 0.28 0.0 530.1 12.3 0.0 0.0 107.0 10.5 0.0 xGlycerol 0.28 0.0 1337.0 7.3 0.0 0.0 2004.9 11.3 0.0 x Lysine 0.26 0.01877.4 43.5 0.0 0.0 604.4 42.6 0.0 x Leucine 0.24 0.0 112.4 12.6 9.7 0.081.7 13.9 11.5 x Sucrose 0.22 0.0 883.3 45.5 13.4 0.0 5926.7 68.3 14.6 xXylose 0.22 0.0 3078.9 77.0 0.0 0.0 1870.0 84.2 0.0 x Acetate 0.21 0.012892.6 85.6 33.1 0.0 6645.0 84.8 36.8 x Guanidoacetate 0.20 0.0 1057.1147.3 98.3 0.0 1145.0 162.8 118.6 x Glycolate 0.20 0.0 1781.0 204.0143.0 0.0 2980.5 228.6 162.6 x Pantothenate 0.19 0.0 536.1 21.7 13.2 0.0177.5 17.9 11.6 x Succinate 0.16 0.0 536.6 39.0 22.5 0.0 269.3 33.7 24.2x Glutamine 0.13 0.0 2004.7 149.7 81.6 0.0 1121.2 176.9 125.8 x1-Methyl- 0.08 0.0 2763.6 35.7 13.8 0.0 381.5 21.7 14.3 x nicotinamide2-Oxoglutarate 0.00 0.0 1256.7 56.2 27.0 0.0 488.8 56.2 30.0 x

TABLE 4 Sensitivity and specificity data (Normal group vs. Polyp group)Training Set Testing Set Model Cutoff Sensitivity Specificity ROC CurveR2Y Q2 Sensitivity Specificity main model 0.297766 88.56% 50.24% 0.76730.194 0.115 74.79% 51.66% 0.358217 78.39% 62.32% 67.23% 59.24% 0.39802368.22% 68.01% 57.98% 68.25% 0.639182 15.68% 97.16% 6.72% 96.21% top 150.301863 74.58% 50.00% 0.6763 0.0749 0.0564 64.71% 42.18% 0.31984368.64% 55.45% 57.98% 52.61% 0.339898 63.14% 62.80% 51.26% 62.09%0.621478 8.47% 97.16% 3.36% 98.10% top 14 0.304827 74.58% 50.47% 0.6750.0716 0.0541 63.87% 43.13% 0.320823 68.22% 55.45% 58.82% 52.61%0.340114 62.71% 62.56% 51.26% 62.09% 0.621743 7.63% 97.16% 3.36% 98.58%top 13 0.305219 75.85% 50.47% 0.6802 0.0735 0.0564 67.23% 44.55%0.323129 68.22% 56.64% 58.82% 54.50% 0.342031 61.86% 61.85% 51.26%63.51% 0.59798 8.90% 97.16% 5.04% 98.10% top 12 0.316487 75.85% 51.66%0.6894 0.0783 0.0595 68.91% 48.82% 0.32912 69.92% 59.48% 62.18% 56.40%0.34476 63.14% 62.80% 52.94% 66.35% 0.589455 9.32% 97.16% 4.20% 98.58%top 11 0.326944 77.97% 50.71% 0.6995 0.0813 0.0589 78.15% 48.82% 0.3431770.34% 60.66% 63.87% 59.24% 0.352496 64.83% 64.45% 55.46% 65.88%0.564702 8.90% 97.16% 5.88% 97.16% top 10 0.341829 79.66% 50.24% 0.70360.0798 0.0537 82.35% 47.39% 0.351485 73.31% 59.24% 69.75% 58.29% 0.3635866.10% 65.88% 55.46% 65.40% 0.521618 10.17% 97.16% 4.20% 95.73% top 90.333275 80.08% 50.00% 0.7037 0.0803 0.0538 78.99% 45.02% 0.34815372.03% 59.72% 62. 18% 58 29% 0.358523 64.83% 64.45% 55.46% 64.93%0.544911 9.75% 97.16% 4.20% 97.63% top 8 0.347543 78.81% 52.84% 0.70710.0799 0.0552 71.43% 50.24% 0.358489 72.03% 62.56% 59.66% 59.72%0.364861 66.53% 66.35% 55.46% 64.45% 0.537677 7.20% 97.16% 5.04% 97.63%top 7 0.378897 78.81% 51.66% 0.6997 0.0641 0.0442 73.95% 50.71% 0.38281471.19% 59.95% 66.39% 58.29% 0.384873 65.68% 65.40% 59.66% 63.51%0.471671 11.02% 97.16% 3.36% 97.63% top 6 0.385209 77.97% 50.95% 0.69580.0574 0.0413 74.79% 50.71% 0.391155 71.19% 61.14% 60.50% 58.77%0.392868 66.95% 66.35% 55.46% 64.45% 0.460474 6.36% 97.16% 4.20% 98.10%top 5 0.379823 71.61% 62.80% 0.6895 0.0552 0.039 53.78% 59.24% 0.38187469.07% 65.17% 51.26% 62.09% 0.383028 66.95% 66.82% 50.42% 63.98%0.472361 5.93% 97.16% 1.68% 96.68% VIP > 1 0.329791 76.69% 51.90% 0.70150.0976 0.0507 65.55% 50.71% 0.339597 70.36% 57.82% 58.82% 56.40%0.352619 64.83% 64.69% 56.30% 64.45% 0.577397 11.44% 97.16% 5.88% 98.58%** Model named VIP > 1 contains 26 metabolites

TABLE 5 VIP scores (Normal group vs. Adenoma group) with concentrationanalysis (concentrations in μM) Normals Adenoma Higher in Higher in VarID (Primary) VIP score min max mean median min max mean median NormalAdenoma Butyrate 3.41 0.0 96.4 3.0 0.0 0.0 10.1 0.1 0.0 x Serine 2.650.0 982.2 87.7 0.0 0.0 664.1 50.5 0.0 x Methanol 2.29 0.0 1054.6 57.321.7 0.0 1019.6 39.8 17.7 x β-Alanine 2.03 0.0 442.9 9.3 0.0 0.0 142.72.0 0.0 x p-Methylhistidine 1.91 0.0 3745.6 227.6 60.4 0.0 3262.4 271.9124.6 x 3-Hydroxybutyrate 1.56 0.0 498.4 11.7 0.0 0.0 3392.5 29.4 0.0 xAsparagine 1.56 0.0 670.6 40.2 0.0 0.0 402.0 45.9 26.9 x Trigonelline1.52 0.0 4771.9 246.5 128.6 0.0 2427.3 295.1 169.6 x 3-Hydroxy- 1.39 0.0188.6 11.9 0.0 0.0 152.3 14.1 0.0 x phenylacetate Histidine 1.37 0.02108.5 208.4 106.5 0.0 3400.1 261.0 155.5 x Acetone 1.34 0.0 115.1 10.06.8 0.0 778.8 14.1 6.0 x 2-Oxoglutarate 1.25 0.0 1256.7 56.2 27.0 0.0553.6 48.1 12.0 x Ethanol 1.24 0.0 27789.2 250.7 0.0 0.0 4594.5 53.7 0.0x Adipate 1.23 0.0 103.9 1.3 0.0 0.0 837.7 9.0 0.0 x 3-Hydroxy- 1.22 0.02539.3 60.0 0.0 0.0 1065.4 75.7 0.0 x mandelate Tyrosine 1.20 0.0 551.862.9 42.6 0.0 606.8 73.4 53.4 x Benzoate 1.16 0.0 567.3 3.5 0.0 0.06282.2 46.0 0.0 x Propylene glycol 0.98 0.0 539.8 35.4 10.0 0.0 451.133.5 0.0 x t-Methylhistidine 0.98 0.0 474.7 78.5 48.7 0.0 706.5 95.265.5 x O-Acetylcarnitine 0.97 0.0 321.3 20.3 11.6 0.0 349.9 18.2 10.5 xCreatine 0.96 0.0 10201.1 331.0 58.1 0.0 5572.1 319.9 72.5 x1,6-Anhydro-Î²-D- 0.94 0.0 603.3 64.5 26.9 0.0 1764.1 87.5 35.9 glucosex Creatinine 0.90 193.0 24617.4 5643.3 4234.9 465.5 31595.9 6397.54691.9 x Alanine 0.89 0.0 1431.3 169.3 110.5 6.2 1995.2 182.5 125.7 x3-Aminoiso- 0.82 0.0 1605.2 83.4 36.2 0.0 2222.4 93.3 33.5 x butyrateHypoxanthine 0.82 0.0 1022.5 21.4 9.3 0.0 199.9 21.4 12.7 xDimethylamine 0.76 8.2 1494.3 194.3 135.0 17.9 1146.5 211.5 156.1 xUracil 0.74 0.0 530.1 12.3 0.0 0.0 107.0 9.1 0.0 x Glycerol 0.72 0.01337.0 7.3 0.0 0.0 635.5 3.9 0.0 x 4-Hydroxy- 0.71 0.0 1401.1 72.6 48.80.0 1354.3 83.4 55.4 x phenylacetate 2-Hydroxy- 0.71 0.0 643.1 30.9 21.62.2 154.8 31.2 24.0 x isobutyrate Threonine 0.66 0.0 976.3 71.2 48.9 0.0430.8 70.3 53.6 x Ascorbate 0.65 0.0 12949.8 276.2 29.8 0.0 10663.2284.3 0.0 x 3-Indoxylsulfate 0.62 0.0 1317.6 120.5 82.5 0.0 845.6 121.089.9 x Urea 0.62 6976.6 441697.0 127007.5 111896.6 19467.8 410148.3130697.5 123744.3 x Isoleucine 0.58 0.0 31.5 4.1 0.0 0.0 69.6 4.0 0.0 xPantothenate 0.55 0.0 536.1 21.7 13.2 0.0 468.1 21.6 10.8 xcis-Aconitate 0.52 0.0 864.8 140.3 79.4 0.0 1275.6 170.8 103.9 x Sucrose0.51 0.0 888.3 45.5 13.4 0.0 1091.4 48.3 0.0 x Citrate 0.50 0.0 15102.42099.7 1563.5 0.0 8519.8 1928.5 1180.5 x Hippurate 0.46 19.0 45262.71675.2 862.7 0.0 10889.5 1802.3 935.4 x Trimethylamine 0.45 0.0 66.4 9.56.5 0.0 270.7 10.9 6.9 x 1-Methyl- 0.45 0.0 2763.6 35.7 13.8 0.0 942.826.5 13.7 x nicotinamide Glucose 0.43 0.0 13433.0 293.2 114.4 0.039542.0 711.4 119.3 x 3-Hydroxy- 0.40 0.0 243.3 31.3 21.9 0.0 141.5 30.924.7 x isovalerate Leucine 0.39 0.0 112.4 12.6 9.7 0.0 81.7 13.3 9.8 xN,N-Dimeth- 0.39 0.0 131.3 24.7 17.5 0.0 387.6 28.2 17.0 x ylglycineSuccinate 0.38 0.0 536.6 39.0 22.5 0.0 291.3 34.3 20.5 x Formate 0.385.1 772.6 121.1 96.0 0.0 1424.0 131.4 101.0 x trans-Aconitate 0.35 0.0456.2 29.1 18.4 0.0 449.7 33.6 18.3 x Tartrate 0.33 0.0 4024.6 104.712.2 0.0 2263.2 116.3 11.2 x Carnitine 0.33 0.0 907.1 47.8 22.7 0.0347.3 46.1 29.7 x Guanidoacetate 0.23 0.0 1057.1 147.3 98.3 0.0 1145.0142.3 95.8 x Glycolate 0.22 0.0 1781.0 204.0 143.0 0.0 1017.4 208.6153.6 x Taurine 0.21 0.0 5028.3 283.2 132.2 0.0 1715.0 285.6 159.2 xPyruvate 0.20 0.0 282.0 17.9 10.7 0.0 390.5 20.8 11.4 x Acetate 0.20 0.012892.6 85.6 33.1 0.0 6645.0 103.4 36.3 x Xylose 0.18 0.0 3078.9 77.00.0 0.0 1914.4 82.5 0.0 x Mannitol 0.15 0.0 4738.5 224.5 0.0 0.0 4200.6221.9 0.0 x Methylguanidine 0.15 0.0 415.5 29.4 17.3 0.0 250.0 28.5 20.6x Lysine 0.14 0.0 1877.4 43.5 0.0 0.0 604.4 40.7 0.0 x Betaine 0.13 0.02675.7 90.9 51.9 0.0 969.5 82.8 52.2 x Valine 0.13 0.0 113.8 20.3 14.20.0 151.2 22.0 16.4 x Lactate 0.12 0.0 2897.0 97.8 52.0 0.0 5581.3 144.250.9 x Glycine 0.07 27.8 4976.9 699.3 506.0 42.9 8600.5 768.0 480.4 xTrimethylamine 0.06 7.1 8301.4 308.6 163.1 0.0 1478.1 265.2 194.8 xN-oxide Pyroglutamate 0.04 0.0 917.4 126.6 92.8 0.0 587.5 133.2 100.8 xGalactose 0.03 0.0 614.8 12.8 0.0 0.0 487.3 9.7 0.0 x Glutamine 0.00 0.02004.7 149.7 81.6 0.0 1121.2 169.8 116.0 x

TABLE 6 Sensitivity and specificity data (Normal group vs. Adenomagroup) Training Set Validation Set Model Cutoff Sensitivity SpecificityROC Curve R2Y Q2 Sensitivity Specificity Main Model 0.25947 88.89%50.24% 0.7524 0.142 0.0463 82.72% 51.18% 0.294233 77.78% 60.19% 75.31%59.24% 0.322602 66.67% 66.59% 67.90% 67.77% 0.527314 11.11% 97.16% 2.47%97.16% Top 15 0.274543 77.78% 50.95% 0.6966 0.0737 0.0398 76.54% 49.76%0.28085 70.37% 57.82% 69.14% 59.72% 0.285875 62.35% 62.32% 59.26% 64.45%0.405516 12.35% 97.16% 2.47% 96.68% Top 14 0.278997 77.78% 52.37% 0.69770.0738 0.0426 75.31% 49.29% 0.284213 70.37% 57.82% 69.14% 56.87%0.288594 62.35% 61.85% 59.26% 63.03% 0.411351 9.88% 96.92% 1.23% 97.63%Top 13 0.281655 77.78% 50.95% 0.6966 0.0676 0.039 74.07% 48.82% 0.28745470.37% 57.82% 67.90% 56.87% 0.29164 62.35% 62.32% 59.26% 62.56% 0.4192667.41% 97.16% 1.23% 97.63% Top 12 0.279368 78.40% 50.71% 0.6978 0.06790.0366 77.78% 48.82% 0.285647 70.37% 58.53% 71.60% 56.87% 0.29013 62.35%62.32% 61.73% 63.03% 0.422674 7.41% 97.16% 1.23% 97.63% Top 11 0.27389979.01% 50.24% 0.6909 0.0657 0.0377 81.48% 51.18% 0.27869 71.60% 56.64%76.54% 54.98% 0.286068 63.58% 63.03% 59.26% 63.51% 0.419749 7.41% 97.16%1.23% 97.63% Top 10 0.277371 78.40% 50.47% 0.6929 0.0655 0.0386 79.01%51.66% 0.28425 70.99% 60.43% 71.60% 57.82% 0.289461 63.58% 63.27% 61.73%62.56% 0.431667 7.41% 97.16% 1.23% 98.10% Top 9 0.292693 75.31% 50.95%0.681 0.056 0.0311 74.07% 49.29% 0.295476 68.52% 56.64% 66.67% 53.55%0.298941 63.58% 62.80% 61.73% 61.61% 0.387558 7.41% 97.16% 1.23% 97.63%Top 8 0.296909 73.46% 50.24% 0.6757 0.0534 0.0317 74.07% 53.55% 0.30052166.05% 58.06% 67.90% 58.77% 0.302474 62.96% 62.80% 59.26% 61.14% 0.373039.26% 97.16% 0.00% 97.63% Top 7 0.304543 74.69% 50.24% 0.6747 0.04650.0313 71.60% 51.66% 0.308861 68.52% 58.77% 65.43% 57.35% 0.31025563.58% 63.51% 60.49% 60.19% 0.353752 6.79% 97.16% 1.23% 97.63% Top 60.30621 73.46% 50.47% 0.6614 0.0404 0.027 71.60% 52.13% 0.310248 67.28%54.27% 67.90% 55.45% 0.312955 60.49% 60.43% 60.49% 61.14% 0.342299 4.94%97.16% 2.47% 96.21% Top 5 0.304164 73.46% 50.00% 0.6581 0.0362 0.02972.84% 51.66% 0.309997 66.67% 54.50% 69.14% 55.45% 0.312623 61.11%60.90% 60.49% 60.19% 0.33285 7.41% 97.16% 2.47% 96.68% VIP > 1 0.25830777.78% 50.47% 0.6937 0.0801 0.0408 82.72% 49.76% 0.26743 69.14% 56.87%72.84% 59.24% 0.274993 61.73% 61.61% 61.73% 64.93% 0.444394 11.73%97.16% 3.70% 97.16% ** Model named VIP > 1 contains 17 metabolites

TABLE 7 Vectors Unique for OPLS/O2PLS Vector Description To Matrix ofscores that summarizes the X variation orthogonal to Y. Tocv Matrix ofcross validated orthogonal scores To ToPS Matrix of scores thatsummarizes the X variation orthogonal to Y for the predictionset. ToPScvMatrix of cross validated predicted scores ToPS for the predictionset.Uo Matrix of scores that summarizes the Y variation orthogonal to X. PoOrthogonal loadings of the X-part of the model. Po expresses theimportance of the variables in approximating X variation orthogonal toY, in the selected component. Po(corr) Orthogonal loadings Po, scaled asthe correlation coefficient between X and To, in the selected component.Pocv Orthogonal loadings Po from the X-part of the model, for a selectedmodel dimension, computed from the selected cross validation round. WoWeights that combine the X variables (first dimension) or the Xresiduals (subsequent dimensions) to form the scores To. These weightsare selected so as to minimize the correlation between To and U, therebyindirectly between To and Y. Wocv Orthogonal weights Wo from the X-partof the model, for a selected model dimension, computed from the selectedcross validation round. Qo Orthogonal loadings of the Y-part of themodel. Qo expresses the importance of the variables in approximating Yvariation orthogonal to X, in the selected component. Qocv Orthogonalloadings Qo from the Y-part of the model, for a selected modeldimension, computed from the selected cross validation round. Co Weightsthat combine the Y variables (first dimension) or the Y residuals(subsequent dimensions) to form the scores Uo. These weights areselected so as to minimize the correlation between Uo and T, therebyindirectly between Uo and X. Cocv Orthogonal weights Co from the Y-partof the model, for a selected model dimension, computed from the selectedcross validation round. Q Loadings of the Y-part of the model. Qexpresses the importance of the variables in approximating Y variationcorrelated to X, in the selected component. Y variables with large Q(positive or negative) are highly correlated with T (and X). QcvLoadings Q from the Y-part of the model, for a selected model dimension,computed from the selected cross validation round. R R is the projectionof Uo on X. R contains non-zero entries when the score matrix Uo is notcompletely orthogonal to X. The norm of this matrix is usually verysmall but is used to enhance the predictions of X. S S is the projectionof To on Y. S contains non-zero entries when the score matrix To is notcompletely orthogonal to Y. The norm of this matrix is usually verysmall but is used to enhance the predictions of Y. Y-Related ProfilesDisplay the estimated pure profiles of the underlying constituents in Xunder the assumption of additive Y-variables.

The invention claimed is:
 1. A method for determining the presence ofcolorectal adenomatous polyps in a subject, said method comprising: a.obtaining a first metabolite profile from a first urine sample collectedfrom the subject, wherein said first metabolite profile is obtained bymeasuring the concentration of any three or more metabolites selectedfrom 1,6-anhydro-β-d-glucose, 1-methylnicotinamide,2-hydroxyisobutyrate, 2-oxoglutarate, 3-aminoisobutyrate,3-hydroxybutyrate, 3-hydroxyisovalerate, 3-hydroxymandelate,3-hydroxyphenylacetate, 3-indoxylsulfate, 4-hydroxyphenylacetate,acetate, acetone, adipate, alanine, ascorbate, asparagine, benzoate,betaine, butyrate, carnitine, citrate, creatine, creatinine,dimethylamine, ethanol, formate, galactose, glucose, glutamine,glycerol, glycine, glycolate, guanidoacetate, hippurate, histidine,hypoxanthine, isoleucine, lactate, leucine, lysine, mannitol, methanol,methylguanidine, n,n-dimethylglycine, o-acetylcarnitine, pantothenate,propylene glycol, pyroglutamate, pyruvate, serine, succinate, sucrose,tartrate, taurine, threonine, trigonelline, trimethylamine,trimethylamine n-oxide, tyrosine, uracil, urea, valine, xylose,cis-aconitate, β-alanine, p-methylhistidine, t-methylhistidine, andtrans-aconitate, b. comparing said first metabolite profile with areference metabolite profile; c. determining the presence of colorectaladenomatous polyps in the subject based on the comparison in step (b);and d. performing a surgical removal of the colorectal polyps in thesubject determined to have adenomatous colorectal polyps.
 2. The methodof claim 1, wherein step (a) comprises measuring the concentration insaid first urine sample of any 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26 metabolites selectedfrom the group consisting of: butyrate; serine; asparagine;p-methylhistidine; 3-hydroxybutyrate; methanol; 3-hydroxymandelate;tyrosine; trigonelline; ß-alanine; histidine; dimethylamine; urea;1,6-anhydro-ß-D-glucose; glucose; ethanol; benzoate; acetone; threonine;2-hydroxyisobutyrate; creatinine; 3-hydroxyphenylacetate;3-indoxylsulfate; hippurate; ascorbate; and 4-hydroxyphenylacetate. 3.The method according to claim 1, wherein: in step (b), said referencemetabolite profile is determined from the concentration of metabolitesin urine of individuals in a reference population corresponding to thosemetabolites measured in step (a).
 4. The method according to claim 1,wherein either or both of said first metabolite profile and saidreference metabolite profile are obtained using one or more methodsselected from the group consisting of: nuclear magnetic resonance (NMR)spectroscopy; high performance liquid chromatography (HPLC); gaschromatography; thin layer chromatography; electrochemical analysis;mass spectroscopy; refractive index spectroscopy; ultra-violetspectroscopy; fluorescent analysis; radiochemical analysis;near-infrared spectroscopy; gas chromatography, and light scatteringanalysis.
 5. The method according to claim 1, wherein multivariatestatistical analysis and/or a mathematical method is used in step (c).6. The method according to claim 5, wherein said multivariatestatistical analysis or mathematical method comprises use of one or moreof PCA, PLS-DA, OPLS, SVM, discriminant analysis, kernel methods,nonparametric methods, tree-based methods, generalized linear models,generalized additive modes, fuzzy logic based methods, neural networks,or genetic algorithm-based methods.
 7. The method of claim 1, whereinthe concentrations of the metabolites are measured using nuclearmagnetic resonance (NMR) spectroscopy.
 8. The method of claim 1, whereinthe subject does not have symptoms of colorectal polyps.